Query 003176
Match_columns 842
No_of_seqs 409 out of 1804
Neff 7.7
Searched_HMMs 46136
Date Thu Mar 28 18:29:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003176.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003176hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 9.2E-71 2E-75 649.9 45.1 472 273-766 72-623 (846)
2 cd06410 PB1_UP2 Uncharacterize 100.0 4.4E-32 9.6E-37 239.9 10.9 91 14-105 1-97 (97)
3 PF10551 MULE: MULE transposas 99.9 2E-21 4.3E-26 174.0 9.4 90 471-562 1-93 (93)
4 PF00872 Transposase_mut: Tran 99.8 2.4E-20 5.1E-25 209.0 3.4 227 372-647 112-350 (381)
5 PF03108 DBD_Tnp_Mut: MuDR fam 99.6 8.7E-16 1.9E-20 128.5 8.9 67 272-338 1-67 (67)
6 COG3328 Transposase and inacti 99.5 4.4E-13 9.5E-18 147.6 17.4 224 372-646 98-328 (379)
7 smart00666 PB1 PB1 domain. Pho 99.0 1.5E-09 3.2E-14 94.5 9.3 76 26-104 3-80 (81)
8 smart00575 ZnF_PMZ plant mutat 98.7 5.3E-09 1.1E-13 71.0 2.3 27 724-750 1-27 (28)
9 PF08731 AFT: Transcription fa 98.7 8.4E-08 1.8E-12 85.7 8.9 68 281-348 1-110 (111)
10 cd05992 PB1 The PB1 domain is 98.5 8E-07 1.7E-11 77.2 8.9 74 28-104 4-80 (81)
11 PF00564 PB1: PB1 domain; Int 98.4 9.4E-07 2E-11 77.3 7.8 76 28-105 5-82 (84)
12 PF03101 FAR1: FAR1 DNA-bindin 98.3 1.4E-06 3E-11 77.5 6.8 59 289-348 1-88 (91)
13 cd06407 PB1_NLP A PB1 domain i 98.3 3.9E-06 8.5E-11 72.6 8.8 73 29-104 5-80 (82)
14 PF04434 SWIM: SWIM zinc finge 97.8 1E-05 2.2E-10 60.2 2.5 30 719-748 10-39 (40)
15 cd06398 PB1_Joka2 The PB1 doma 97.7 0.00028 6.1E-09 62.3 9.6 75 28-105 4-87 (91)
16 cd06408 PB1_NoxR The PB1 domai 97.7 0.00015 3.2E-09 62.8 7.4 57 33-93 10-66 (86)
17 cd06405 PB1_Mekk2_3 The PB1 do 97.6 0.00046 1E-08 56.9 8.3 70 29-105 5-77 (79)
18 cd06406 PB1_P67 A PB1 domain i 97.5 0.00031 6.8E-09 59.7 7.3 65 28-96 6-70 (80)
19 cd06397 PB1_UP1 Uncharacterize 97.3 0.0011 2.5E-08 55.7 7.3 65 29-96 5-69 (82)
20 cd06401 PB1_TFG The PB1 domain 97.1 0.0035 7.6E-08 53.4 8.6 69 33-104 8-80 (81)
21 cd06404 PB1_aPKC PB1 domain is 97.1 0.0039 8.4E-08 53.3 8.7 61 32-94 7-68 (83)
22 cd06403 PB1_Par6 The PB1 domai 96.9 0.0071 1.5E-07 51.0 8.9 71 31-105 6-78 (80)
23 cd06402 PB1_p62 The PB1 domain 96.8 0.0074 1.6E-07 52.7 8.8 68 35-105 15-85 (87)
24 cd06396 PB1_NBR1 The PB1 domai 96.8 0.0041 8.9E-08 53.3 7.0 69 33-105 8-79 (81)
25 cd06411 PB1_p51 The PB1 domain 96.7 0.0074 1.6E-07 51.1 7.2 63 35-97 7-69 (78)
26 cd06409 PB1_MUG70 The MUG70 pr 95.8 0.059 1.3E-06 47.0 8.5 71 32-104 8-83 (86)
27 PF00098 zf-CCHC: Zinc knuckle 94.6 0.02 4.3E-07 34.7 1.5 18 823-840 1-18 (18)
28 PF06782 UPF0236: Uncharacteri 94.5 0.63 1.4E-05 54.2 14.6 129 504-645 235-376 (470)
29 PF13610 DDE_Tnp_IS240: DDE do 93.5 0.037 8.1E-07 53.3 1.8 81 464-548 1-81 (140)
30 PF01610 DDE_Tnp_ISL3: Transpo 93.2 0.14 3E-06 54.2 5.7 94 467-566 1-97 (249)
31 PF15288 zf-CCHC_6: Zinc knuck 92.7 0.051 1.1E-06 39.8 1.0 19 823-841 2-22 (40)
32 PF13696 zf-CCHC_2: Zinc knuck 89.9 0.19 4.1E-06 35.1 1.5 21 821-841 7-27 (32)
33 PF03106 WRKY: WRKY DNA -bindi 89.2 0.75 1.6E-05 37.4 4.7 39 310-348 21-59 (60)
34 COG3316 Transposase and inacti 88.2 4.5 9.7E-05 41.6 10.6 120 383-551 33-152 (215)
35 PF04684 BAF1_ABF1: BAF1 / ABF 85.4 1.7 3.7E-05 48.9 6.2 57 276-332 23-80 (496)
36 PF04500 FLYWCH: FLYWCH zinc f 85.4 1.5 3.3E-05 35.2 4.6 46 298-347 14-62 (62)
37 cd06399 PB1_P40 The PB1 domain 84.9 3 6.6E-05 36.1 6.2 60 33-96 12-75 (92)
38 cd01799 Hoil1_N Ubiquitin-like 84.2 3.1 6.7E-05 35.5 6.1 38 32-70 10-47 (75)
39 PF00665 rve: Integrase core d 83.1 6.1 0.00013 36.1 8.3 76 463-539 5-81 (120)
40 cd01796 DDI1_N DNA damage indu 82.6 2.3 5E-05 35.7 4.6 38 33-70 8-45 (71)
41 cd01807 GDX_N ubiquitin-like d 81.4 3.3 7.1E-05 35.0 5.2 42 29-70 5-46 (74)
42 cd01812 BAG1_N Ubiquitin-like 81.4 2.9 6.4E-05 34.7 4.9 41 29-70 5-45 (71)
43 PF11976 Rad60-SLD: Ubiquitin- 81.1 3.7 8E-05 34.3 5.4 41 29-69 5-46 (72)
44 PF14560 Ubiquitin_2: Ubiquiti 80.7 2.8 6.1E-05 36.7 4.7 46 39-84 18-63 (87)
45 PHA02517 putative transposase 80.4 17 0.00036 39.1 11.7 152 360-538 30-182 (277)
46 cd01809 Scythe_N Ubiquitin-lik 79.9 4.2 9.1E-05 33.8 5.4 41 29-69 5-45 (72)
47 cd01794 DC_UbP_C dendritic cel 79.5 3.6 7.9E-05 34.5 4.8 43 28-70 2-44 (70)
48 PRK14702 insertion element IS2 79.0 49 0.0011 35.4 14.5 145 358-537 10-164 (262)
49 cd01798 parkin_N amino-termina 78.9 4.1 9E-05 33.9 5.0 42 29-70 3-44 (70)
50 PF03050 DDE_Tnp_IS66: Transpo 78.7 3.5 7.6E-05 44.2 5.7 133 373-567 19-156 (271)
51 cd01803 Ubiquitin Ubiquitin. U 77.8 4.6 0.0001 33.9 5.0 41 29-69 5-45 (76)
52 cd00196 UBQ Ubiquitin-like pro 77.4 5.3 0.00012 30.8 5.1 47 29-75 2-48 (69)
53 smart00774 WRKY DNA binding do 77.4 3.2 7E-05 33.6 3.6 38 310-347 21-59 (59)
54 PRK09409 IS2 transposase TnpB; 76.0 66 0.0014 35.2 14.7 143 360-537 51-203 (301)
55 PTZ00044 ubiquitin; Provisiona 75.3 6.3 0.00014 33.3 5.2 42 29-70 5-46 (76)
56 PF13565 HTH_32: Homeodomain-l 74.2 4.9 0.00011 34.0 4.3 41 360-400 34-76 (77)
57 smart00343 ZnF_C2HC zinc finge 74.1 1.6 3.4E-05 29.0 0.9 17 824-840 1-17 (26)
58 PF14392 zf-CCHC_4: Zinc knuck 73.2 1.3 2.8E-05 34.4 0.4 19 822-840 31-49 (49)
59 cd01800 SF3a120_C Ubiquitin-li 72.1 6.9 0.00015 33.3 4.7 39 32-70 5-43 (76)
60 PF04937 DUF659: Protein of un 71.8 55 0.0012 32.0 11.5 63 505-567 73-138 (153)
61 cd01806 Nedd8 Nebb8-like ubiq 71.5 9.8 0.00021 31.9 5.5 42 29-70 5-46 (76)
62 cd01763 Sumo Small ubiquitin-r 69.8 9.1 0.0002 33.5 5.0 45 26-70 13-57 (87)
63 PF11470 TUG-UBL1: GLUT4 regul 69.3 7.6 0.00016 32.2 4.1 39 32-70 4-42 (65)
64 cd01805 RAD23_N Ubiquitin-like 69.2 12 0.00025 31.7 5.5 42 29-70 5-48 (77)
65 cd01810 ISG15_repeat2 ISG15 ub 68.8 10 0.00022 32.0 4.9 42 29-70 3-44 (74)
66 COG5431 Uncharacterized metal- 68.5 9.1 0.0002 34.3 4.6 29 714-744 42-75 (117)
67 cd01769 UBL Ubiquitin-like dom 67.9 13 0.00028 30.2 5.4 41 30-70 3-43 (69)
68 smart00213 UBQ Ubiquitin homol 66.6 13 0.00029 29.6 5.2 41 29-70 5-45 (64)
69 cd01789 Alp11_N Ubiquitin-like 66.6 13 0.00028 32.4 5.2 47 39-86 17-63 (84)
70 cd06395 PB1_Map2k5 PB1 domain 65.9 13 0.00029 31.6 4.8 49 43-94 21-69 (91)
71 cd01793 Fubi Fubi ubiquitin-li 63.4 16 0.00035 30.7 5.2 40 31-70 5-44 (74)
72 cd01813 UBP_N UBP ubiquitin pr 61.8 18 0.0004 30.6 5.2 37 33-69 8-44 (74)
73 cd01802 AN1_N ubiquitin-like d 60.8 17 0.00038 33.0 5.2 42 29-70 32-73 (103)
74 COG5179 TAF1 Transcription ini 57.7 6.2 0.00013 45.8 2.0 23 819-841 934-958 (968)
75 PF02178 AT_hook: AT hook moti 55.8 5.1 0.00011 22.3 0.5 9 803-811 2-10 (13)
76 cd01804 midnolin_N Ubiquitin-l 53.9 29 0.00063 29.6 5.2 41 30-70 7-47 (78)
77 PF00240 ubiquitin: Ubiquitin 52.1 34 0.00075 28.0 5.3 39 32-70 3-41 (69)
78 PF14847 Ras_bdg_2: Ras-bindin 50.4 50 0.0011 30.1 6.3 80 29-108 5-89 (105)
79 smart00384 AT_hook DNA binding 43.5 13 0.00029 24.6 1.0 12 802-813 1-12 (26)
80 cd01797 NIRF_N amino-terminal 42.7 45 0.00098 28.5 4.6 41 30-70 6-48 (78)
81 COG4279 Uncharacterized conser 39.9 14 0.0003 38.6 1.1 23 724-749 125-147 (266)
82 PRK09335 30S ribosomal protein 39.3 23 0.00051 31.4 2.3 27 799-830 2-28 (95)
83 cd01791 Ubl5 UBL5 ubiquitin-li 38.7 62 0.0013 27.3 4.8 38 33-70 10-47 (73)
84 PF13917 zf-CCHC_3: Zinc knuck 37.9 17 0.00036 27.4 1.0 19 822-840 4-22 (42)
85 cd01808 hPLIC_N Ubiquitin-like 37.3 67 0.0014 26.7 4.8 36 33-69 9-44 (71)
86 cd01792 ISG15_repeat1 ISG15 ub 37.1 59 0.0013 27.8 4.5 38 30-67 8-45 (80)
87 PLN00186 ribosomal protein S26 33.7 31 0.00068 31.3 2.2 27 799-830 2-28 (109)
88 PTZ00172 40S ribosomal protein 33.3 32 0.0007 31.2 2.2 27 799-830 2-28 (108)
89 PF05741 zf-nanos: Nanos RNA b 31.8 18 0.00038 28.9 0.3 20 821-840 32-54 (55)
90 PF14201 DUF4318: Domain of un 31.6 68 0.0015 27.3 3.8 29 280-308 13-41 (74)
91 KOG3206 Alpha-tubulin folding 30.3 61 0.0013 33.0 3.8 62 41-106 19-80 (234)
92 COG5082 AIR1 Arginine methyltr 29.8 27 0.00058 35.2 1.3 16 823-838 98-113 (190)
93 PF13592 HTH_33: Winged helix- 29.8 58 0.0013 26.3 3.0 28 373-400 3-30 (60)
94 PHA00689 hypothetical protein 29.6 29 0.00062 26.6 1.1 14 819-832 14-27 (62)
95 PF11543 UN_NPL4: Nuclear pore 29.4 55 0.0012 28.2 3.0 29 39-67 18-46 (80)
96 PF12762 DDE_Tnp_IS1595: ISXO2 28.7 1.2E+02 0.0027 29.0 5.8 69 465-538 4-87 (151)
97 PRK13907 rnhA ribonuclease H; 27.3 4.8E+02 0.011 24.0 9.4 77 466-545 3-81 (128)
98 cd01760 RBD Ubiquitin-like dom 25.8 1.2E+02 0.0026 25.6 4.4 37 33-69 8-44 (72)
99 KOG1769 Ubiquitin-like protein 24.9 1.5E+02 0.0032 26.7 4.9 38 32-69 28-65 (99)
100 KOG3606 Cell polarity protein 24.6 90 0.002 33.1 4.0 85 33-121 26-112 (358)
101 COG4715 Uncharacterized conser 24.2 1.7E+02 0.0037 34.4 6.5 44 707-752 50-99 (587)
102 smart00455 RBD Raf-like Ras-bi 23.5 1.4E+02 0.0031 24.9 4.4 36 34-69 9-44 (70)
103 PF02196 RBD: Raf-like Ras-bin 23.2 1.2E+02 0.0027 25.4 4.0 34 34-67 10-43 (71)
104 PRK12286 rpmF 50S ribosomal pr 22.8 77 0.0017 25.5 2.5 34 799-832 4-37 (57)
105 PF04800 ETC_C1_NDUFA4: ETC co 22.4 1.1E+02 0.0024 27.7 3.7 29 277-309 51-79 (101)
106 PF01498 HTH_Tnp_Tc3_2: Transp 22.3 56 0.0012 27.2 1.7 36 365-401 4-39 (72)
107 PF08459 UvrC_HhH_N: UvrC Heli 20.6 3.1E+02 0.0067 27.0 6.7 64 466-547 32-101 (155)
108 COG5082 AIR1 Arginine methyltr 20.6 45 0.00098 33.6 0.9 19 821-839 59-77 (190)
109 PF13877 RPAP3_C: Potential Mo 20.3 71 0.0015 28.2 2.1 34 588-621 5-38 (94)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=9.2e-71 Score=649.91 Aligned_cols=472 Identities=16% Similarity=0.243 Sum_probs=374.6
Q ss_pred CCCCCCceeCCHHHHHHHHHHHHHhcceeEEEEeeCcc-------EEEEEec----------------------------
Q 003176 273 SITGVGQEFKSVIEFRDALQRFSIAHRFRYKFKKNETS-------RASGMCA---------------------------- 317 (842)
Q Consensus 273 ~~~~vG~~F~s~ee~k~ai~~yAi~~gf~~r~~ks~~~-------r~~~~C~---------------------------- 317 (842)
..+.+||+|+|.+|++.+|+.||...||.+|+.++.++ ..+++|+
T Consensus 72 ~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~~~~~ 151 (846)
T PLN03097 72 LEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDPENGT 151 (846)
T ss_pred ccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCccccc
Confidence 35789999999999999999999999999998654322 1245554
Q ss_pred ------CCCCceEEEEEEeCCcceEEEEeecCCCccC--CCCCCCCccchhhHHHHHhHhhcCCCCChhHHHHHHHHhcC
Q 003176 318 ------AEGCSWSFYASWVPSERVFKIKKMNETHTCG--ESSKTAHPTKNWLVSIIKDKLRESPHHKPKEISKSILRDFG 389 (842)
Q Consensus 318 ------~~gCpwri~as~~~~~~~w~I~~~~~~HnC~--~~~~~~~~t~~~ia~~~~~~l~~~~~~~~~~I~~~l~~~~g 389 (842)
++||+++|++++.. .+.|+|+.+..+|||+ +.......+++.+....+ .+....++ . .++.+.
T Consensus 152 ~rR~~tRtGC~A~m~Vk~~~-~gkW~V~~fv~eHNH~L~p~~~~~~~~r~~~~~~~~-~~~~~~~v-----~-~~~~d~- 222 (846)
T PLN03097 152 GRRSCAKTDCKASMHVKRRP-DGKWVIHSFVKEHNHELLPAQAVSEQTRKMYAAMAR-QFAEYKNV-----V-GLKNDS- 222 (846)
T ss_pred ccccccCCCCceEEEEEEcC-CCeEEEEEEecCCCCCCCCccccchhhhhhHHHHHh-hhhccccc-----c-ccchhh-
Confidence 34799999998754 4689999999999999 322211111111111000 00000000 0 000000
Q ss_pred cccchhhhHHHHHHHHHhhhCCHHHHhhchHHHHHHHHHhCCCcEEEEEecCCcceeEEEEEehhhHHHHHhcCCCeEEe
Q 003176 390 VTLNYSQVYRGIEGAREQLQGSYKEAYNQLPWFCDKLLEANPGSFIKLLIDNDKKFQRLFISFDASIHGFQNGCRPLLFL 469 (842)
Q Consensus 390 ~~~sy~~~~rak~~a~~~~~g~~~esy~~L~~y~~~l~~~NPg~~~~v~~d~d~~f~~lF~a~~~s~~~f~~~~~~vl~i 469 (842)
.++ .-+.+... +. ......|..||+++++.||+|+|++++|++++++++|||++.|+.+|.+ |+|||.|
T Consensus 223 --~~~--~~~~r~~~---~~---~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWaD~~sr~~Y~~-FGDvV~f 291 (846)
T PLN03097 223 --KSS--FDKGRNLG---LE---AGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWVDAKSRHDYGN-FSDVVSF 291 (846)
T ss_pred --cch--hhHHHhhh---cc---cchHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEeccHHHHHHHHh-cCCEEEE
Confidence 001 11111111 11 2245679999999999999999999999999999999999999999999 9999999
Q ss_pred ccccccccccceEEEEEEecCCCCeEEEEEEEecCCChhhHHHHHHHHHHhhcCCCcEEEEecCchhHHHHHHhhcccCc
Q 003176 470 DSTSLRSKYHEILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSSSRSITFVSDKQKGLMESVLKIFENAH 549 (842)
Q Consensus 470 D~T~~~~~y~~~Ll~a~g~D~~~~~~plafalv~~Et~es~~WfL~~lk~~~~~~~p~~iisD~~~~l~~AI~~vfP~a~ 549 (842)
|+||++|+|++||+.++|+|+|+|++++|+||+.+|+.++|.|+|++|+++|++..|.+||||++.+|.+||++|||++.
T Consensus 292 DTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~tIiTDqd~am~~AI~~VfP~t~ 371 (846)
T PLN03097 292 DTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQAPKVIITDQDKAMKSVISEVFPNAH 371 (846)
T ss_pred eceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCCCceEEecCCHHHHHHHHHHCCCce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEecHHHHHHHHHhhcCCCCCccccCchhHHHHHHHH-hhhHHHHHHHHHHHH-hhChhHHHHHHhh--ccccccccccc
Q 003176 550 HGYSIYHLLDNFMKNLKGPFHGEGKGSLPVNFLAAAC-AARLDSFRMSAEQVK-KVSSNAFDWMMQI--APEYWTNAAFK 625 (842)
Q Consensus 550 h~~C~~Hi~~N~~~~~~~~~~~e~k~~~~~~~~~~~~-a~t~~eFe~~~~~l~-~~~~~~~~yL~~~--~~~~Wa~a~f~ 625 (842)
|++|+|||++|+.++++..+.. .+.|...|..+++ +.+++||+..|..|. +++...++||..+ .|++|+++|++
T Consensus 372 Hr~C~wHI~~~~~e~L~~~~~~--~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY~k 449 (846)
T PLN03097 372 HCFFLWHILGKVSENLGQVIKQ--HENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTYMR 449 (846)
T ss_pred ehhhHHHHHHHHHHHhhHHhhh--hhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHHhc
Confidence 9999999999999999875532 3589999999998 679999999999886 4568999999998 99999999999
Q ss_pred cCCcccc-ccchhhhhHHHHhhhh--ccchHHHHHHHHHHHHHHHHhhh--------c---------ccccccccCcchH
Q 003176 626 GESYQHI-TFDVAESYANWIEEVW--ELPLIQKLERLLCKMTEMINNRR--------M---------NSSGWFTKLIPSR 685 (842)
Q Consensus 626 ~~~~~~~-TtN~~Es~N~~lk~~r--~lpi~~lve~ir~~l~~~~~~rr--------~---------~~~~~~~~~tp~~ 685 (842)
+.+++.| ||+++||+|++|++.. ..+|..|++.+...+..+..... . ...+.+..|||.+
T Consensus 450 ~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~iYT~~i 529 (846)
T PLN03097 450 DAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSGVYTHAV 529 (846)
T ss_pred ccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHHHhHHHH
Confidence 8887766 7889999999999864 67888888877665543332111 1 1123478999999
Q ss_pred HHHHHHHHHhccceEEEEeC----CceEEEEc---CceeEee----cCCccccccchhccCCchhhHHHHHHhcCCC--c
Q 003176 686 EQLVKDASRRAHYLKVLFSS----DTLFEVQG---DSTHVVD----MNKRDCSCLVWKATGLPCHHAIAVFNSTGRN--V 752 (842)
Q Consensus 686 ~~kl~~~~~~a~~~~V~~~~----~~~feV~~---~~~~~V~----l~~~~CsC~~~~~~GiPC~Halav~~~~~~~--~ 752 (842)
|++||+++..+..|.+.... ..+|.|.+ ...|.|. ....+|+|++|+..||||+|||.||...++. |
T Consensus 530 F~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~IP 609 (846)
T PLN03097 530 FKKFQVEVLGAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAIP 609 (846)
T ss_pred HHHHHHHHHHhhheEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccCc
Confidence 99999999999888876532 25788865 3456663 2478999999999999999999999999984 9
Q ss_pred cccccccceecccc
Q 003176 753 YDYCSSYFTVDSYR 766 (842)
Q Consensus 753 ~~yv~~~yt~~~~~ 766 (842)
..||.++||.++-.
T Consensus 610 ~~YILkRWTKdAK~ 623 (846)
T PLN03097 610 SQYILKRWTKDAKS 623 (846)
T ss_pred hhhhhhhchhhhhh
Confidence 99999999977654
No 2
>cd06410 PB1_UP2 Uncharacterized protein 2. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=99.97 E-value=4.4e-32 Score=239.92 Aligned_cols=91 Identities=36% Similarity=0.686 Sum_probs=87.7
Q ss_pred EEeeCCeeccCC-CCCeEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCC-CceEeecChHHHHHHH
Q 003176 14 ICQSGGEFVTKD-DGSLSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNK-QTLITICNDKDLKRMF 91 (842)
Q Consensus 14 ~~~~gg~~~~~~-~~~~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~-~~l~~~~~d~dl~~m~ 91 (842)
||||||+|+|++ ||+|+|+||+||+|+|+|+|||+||++||+++++++.+ ++||||||+|+ |+||||++||||.|||
T Consensus 1 ~cs~GG~i~pr~~dg~l~Y~GG~tr~i~V~r~~s~~el~~kl~~~~~~~~~-~~lky~Lp~edld~Lisv~~DeDl~~M~ 79 (97)
T cd06410 1 LCSYGGRILPRPPDGQLRYVGGETRIVSVDRSISFKELVSKLSELFGAGVV-VTLKYQLPDEDLDALISVSNDEDLKNMM 79 (97)
T ss_pred CcccCCEEeCcCCCCCEEEcCCceEEEEEcCCCCHHHHHHHHHHHhCCCCc-eEEEEEcCCCCcceeEEecCcHHHHHHH
Confidence 799999999877 99999999999999999999999999999999998876 99999999999 9999999999999999
Q ss_pred hccC----CceeEEEEEe
Q 003176 92 DFHE----GSVTADVFVI 105 (842)
Q Consensus 92 ~~~~----~~~~~~v~~~ 105 (842)
++++ +++++|||++
T Consensus 80 ~e~~~~~~~~~rirvflf 97 (97)
T cd06410 80 EEYDRLSGGSARLRVFLF 97 (97)
T ss_pred HhhccccCCCceEEEEEC
Confidence 9999 9999999986
No 3
>PF10551 MULE: MULE transposase domain; InterPro: IPR018289 This entry represents a domain found in Mutator-like elements (MULE)-encoded tranposases, some of which also contain a zinc-finger motif [, ]. This domain is also found in a transposase for the insertion sequence element IS256 in transposon Tn4001 [].
Probab=99.85 E-value=2e-21 Score=174.02 Aligned_cols=90 Identities=37% Similarity=0.695 Sum_probs=87.0
Q ss_pred cccccccccceEEE---EEEecCCCCeEEEEEEEecCCChhhHHHHHHHHHHhhcCCCcEEEEecCchhHHHHHHhhccc
Q 003176 471 STSLRSKYHEILLT---ATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSSSRSITFVSDKQKGLMESVLKIFEN 547 (842)
Q Consensus 471 ~T~~~~~y~~~Ll~---a~g~D~~~~~~plafalv~~Et~es~~WfL~~lk~~~~~~~p~~iisD~~~~l~~AI~~vfP~ 547 (842)
|||++|+| ++++. ++|+|++|+.+|+||+++.+|+.++|.|||+.+++.++.. |.+||+|++.|+.+||+++||+
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~-p~~ii~D~~~~~~~Ai~~vfP~ 78 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQK-PKVIISDFDKALINAIKEVFPD 78 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccC-ceeeeccccHHHHHHHHHHCCC
Confidence 79999999 98886 9999999999999999999999999999999999999887 9999999999999999999999
Q ss_pred CceEecHHHHHHHHH
Q 003176 548 AHHGYSIYHLLDNFM 562 (842)
Q Consensus 548 a~h~~C~~Hi~~N~~ 562 (842)
+.|++|.||+.+|++
T Consensus 79 ~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 79 ARHQLCLFHILRNIK 93 (93)
T ss_pred ceEehhHHHHHHhhC
Confidence 999999999999985
No 4
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=99.79 E-value=2.4e-20 Score=209.03 Aligned_cols=227 Identities=21% Similarity=0.266 Sum_probs=182.9
Q ss_pred CCCCChhHHHHHHHHhcC-cccchhhhHHHHHHHHHhhhCCHHHHhhchHHHHHHHHHhCCCcEEEEEecCCcceeEEEE
Q 003176 372 SPHHKPKEISKSILRDFG-VTLNYSQVYRGIEGAREQLQGSYKEAYNQLPWFCDKLLEANPGSFIKLLIDNDKKFQRLFI 450 (842)
Q Consensus 372 ~~~~~~~~I~~~l~~~~g-~~~sy~~~~rak~~a~~~~~g~~~esy~~L~~y~~~l~~~NPg~~~~v~~d~d~~f~~lF~ 450 (842)
-.|++.++|...++.-+| ..+|-+++.|..+...+.+ ..| +...
T Consensus 112 ~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~-----------~~w----~~R~-------------------- 156 (381)
T PF00872_consen 112 LKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEV-----------EAW----RNRP-------------------- 156 (381)
T ss_pred ccccccccccchhhhhhcccccCchhhhhhhhhhhhhH-----------HHH----hhhc--------------------
Confidence 368999999999999999 7899888887665554322 112 1111
Q ss_pred EehhhHHHHHhcC-CCeEEecccccccccc-----ceEEEEEEecCCCCeEEEEEEEecCCChhhHHHHHHHHHHhhcCC
Q 003176 451 SFDASIHGFQNGC-RPLLFLDSTSLRSKYH-----EILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSSS 524 (842)
Q Consensus 451 a~~~s~~~f~~~~-~~vl~iD~T~~~~~y~-----~~Ll~a~g~D~~~~~~plafalv~~Et~es~~WfL~~lk~~~~~~ 524 (842)
.. +. -++|++||+|.+.+.+ ..+++++|+|.+|+..+||+.+...|+.++|.-||+.|++. |..
T Consensus 157 --------L~-~~~y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R-Gl~ 226 (381)
T PF00872_consen 157 --------LE-SEPYPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER-GLK 226 (381)
T ss_pred --------cc-cccccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc-ccc
Confidence 00 13 4789999999997754 46799999999999999999999999999999999999888 445
Q ss_pred CcEEEEecCchhHHHHHHhhcccCceEecHHHHHHHHHhhcCCCCCccccCchhHHHHHHHHhhhHHHHHHHHHHHH---
Q 003176 525 RSITFVSDKQKGLMESVLKIFENAHHGYSIYHLLDNFMKNLKGPFHGEGKGSLPVNFLAAACAARLDSFRMSAEQVK--- 601 (842)
Q Consensus 525 ~p~~iisD~~~~l~~AI~~vfP~a~h~~C~~Hi~~N~~~~~~~~~~~e~k~~~~~~~~~~~~a~t~~eFe~~~~~l~--- 601 (842)
.+..||+|+++||.+||.++||++.++.|.+|+++|+.+++... .++.+...++.+..+.+.++....++.+.
T Consensus 227 ~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~k----~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~~~ 302 (381)
T PF00872_consen 227 DILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPKK----DRKEVKADLKAIYQAPDKEEAREALEEFAEKW 302 (381)
T ss_pred ccceeeccccccccccccccccchhhhhheechhhhhccccccc----cchhhhhhccccccccccchhhhhhhhccccc
Confidence 68999999999999999999999999999999999999998653 44566777777777777777777666654
Q ss_pred -hhChhHHHHHHhhccccccccccccCCc-cccccchhhhhHHHHhhh
Q 003176 602 -KVSSNAFDWMMQIAPEYWTNAAFKGESY-QHITFDVAESYANWIEEV 647 (842)
Q Consensus 602 -~~~~~~~~yL~~~~~~~Wa~a~f~~~~~-~~~TtN~~Es~N~~lk~~ 647 (842)
..+|++.++|.+...+.|+..-|+...+ ...|||.+|++|+.||..
T Consensus 303 ~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr 350 (381)
T PF00872_consen 303 EKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRRR 350 (381)
T ss_pred ccccchhhhhhhhccccccceeeecchhccccchhhhccccccchhhh
Confidence 4679999999998777777665665444 456999999999999764
No 5
>PF03108 DBD_Tnp_Mut: MuDR family transposase; InterPro: IPR004332 The plant MuDR transposase domain is present in plant proteins that are presumed to be the transposases for Mutator transposable elements [, ]. The function of these proteins is unknown. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=99.63 E-value=8.7e-16 Score=128.50 Aligned_cols=67 Identities=33% Similarity=0.635 Sum_probs=65.0
Q ss_pred CCCCCCCceeCCHHHHHHHHHHHHHhcceeEEEEeeCccEEEEEecCCCCceEEEEEEeCCcceEEE
Q 003176 272 DSITGVGQEFKSVIEFRDALQRFSIAHRFRYKFKKNETSRASGMCAAEGCSWSFYASWVPSERVFKI 338 (842)
Q Consensus 272 ~~~~~vG~~F~s~ee~k~ai~~yAi~~gf~~r~~ks~~~r~~~~C~~~gCpwri~as~~~~~~~w~I 338 (842)
||.+.+||+|+|++||+.||..||++++|++++.+|+++|++++|...||||+|+|++.++++.|+|
T Consensus 1 n~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~r~~~~C~~~~C~Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 1 NPELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKKRYRAKCKDKGCPWRVRASKRKRSDTFQI 67 (67)
T ss_pred CCccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCCEEEEEEEcCCCCCEEEEEEEcCCCCEEEC
Confidence 6789999999999999999999999999999999999999999999999999999999999999986
No 6
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.50 E-value=4.4e-13 Score=147.58 Aligned_cols=224 Identities=17% Similarity=0.174 Sum_probs=168.8
Q ss_pred CCCCChhHHHHHHHHhcCcccchhhhHHHHHHHHHhhhCCHHHHhhchHHHHHHHHHhCCCcEEEEEecCCcceeEEEEE
Q 003176 372 SPHHKPKEISKSILRDFGVTLNYSQVYRGIEGAREQLQGSYKEAYNQLPWFCDKLLEANPGSFIKLLIDNDKKFQRLFIS 451 (842)
Q Consensus 372 ~~~~~~~~I~~~l~~~~g~~~sy~~~~rak~~a~~~~~g~~~esy~~L~~y~~~l~~~NPg~~~~v~~d~d~~f~~lF~a 451 (842)
..|++++++...+++.++..++-..+.+......+. +.+++.+-+
T Consensus 98 ~~gv~Tr~i~~~~~~~~~~~~s~~~iS~~~~~~~e~---------------v~~~~~r~l-------------------- 142 (379)
T COG3328 98 AKGVTTREIEALLEELYGHKVSPSVISVVTDRLDEK---------------VKAWQNRPL-------------------- 142 (379)
T ss_pred HcCCcHHHHHHHHHHhhCcccCHHHhhhHHHHHHHH---------------HHHHHhccc--------------------
Confidence 468999999999999998877766665554444332 222222211
Q ss_pred ehhhHHHHHhcCCCeEEecccccccc--ccceEEEEEEecCCCCeEEEEEEEecCCChhhHHHHHHHHHHhhcCCCcEEE
Q 003176 452 FDASIHGFQNGCRPLLFLDSTSLRSK--YHEILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSSSRSITF 529 (842)
Q Consensus 452 ~~~s~~~f~~~~~~vl~iD~T~~~~~--y~~~Ll~a~g~D~~~~~~plafalv~~Et~es~~WfL~~lk~~~~~~~p~~i 529 (842)
+..++|++|++|++-+ -+..+++|+|++.+|+...+++.+-..|+ ..|.-||..|+.. |......+
T Consensus 143 ----------~~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~r-gl~~v~l~ 210 (379)
T COG3328 143 ----------GDYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNR-GLSDVLLV 210 (379)
T ss_pred ----------cCceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhc-cccceeEE
Confidence 2668999999999987 45689999999999999999999999999 9999888888877 33345567
Q ss_pred EecCchhHHHHHHhhcccCceEecHHHHHHHHHhhcCCCCCccccCchhHHHHHHHHhhhHHHHHHH----HHHHHhhCh
Q 003176 530 VSDKQKGLMESVLKIFENAHHGYSIYHLLDNFMKNLKGPFHGEGKGSLPVNFLAAACAARLDSFRMS----AEQVKKVSS 605 (842)
Q Consensus 530 isD~~~~l~~AI~~vfP~a~h~~C~~Hi~~N~~~~~~~~~~~e~k~~~~~~~~~~~~a~t~~eFe~~----~~~l~~~~~ 605 (842)
++|+.+|+.+||.++||.+.++.|..|+.+|+..+.... .++.+...+.....+.+.++-... .+.+...+|
T Consensus 211 v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~k----~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~~yP 286 (379)
T COG3328 211 VVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPRK----DQDAVLSDLRSIYIAPDAEEALLALLAFSELWGKRYP 286 (379)
T ss_pred ecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhhh----hhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhhhcc
Confidence 779999999999999999999999999999999987653 334455555544445555554444 444556779
Q ss_pred hHHHHHHhhccccccccccc-cCCccccccchhhhhHHHHhh
Q 003176 606 NAFDWMMQIAPEYWTNAAFK-GESYQHITFDVAESYANWIEE 646 (842)
Q Consensus 606 ~~~~yL~~~~~~~Wa~a~f~-~~~~~~~TtN~~Es~N~~lk~ 646 (842)
....|+.+..-+.|...-|+ ..+--..|||..|++|+.++.
T Consensus 287 ~i~~~~~~~~~~~~~F~~fp~~~r~~i~ttN~IE~~n~~ir~ 328 (379)
T COG3328 287 AILKSWRNALEELLPFFAFPSEIRKIIYTTNAIESLNKLIRR 328 (379)
T ss_pred hHHHHHHHHHHHhcccccCcHHHHhHhhcchHHHHHHHHHHH
Confidence 99999988866666544443 444567899999999997753
No 7
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=99.01 E-value=1.5e-09 Score=94.46 Aligned_cols=76 Identities=26% Similarity=0.491 Sum_probs=66.6
Q ss_pred CCCeEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCCc--eeEEEE
Q 003176 26 DGSLSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEGS--VTADVF 103 (842)
Q Consensus 26 ~~~~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~~--~~~~v~ 103 (842)
..+++| ||++|.+.|++++||+||+++|++.|++..+.++|||+ .++.-+|++++|+||..|+++...+ ..++|+
T Consensus 3 ~vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~--Dedgd~v~l~sd~Dl~~a~~~~~~~~~~~l~l~ 79 (81)
T smart00666 3 DVKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQ--DEDGDLVSLTSDEDLEEAIEEYDSLGSKKLRLH 79 (81)
T ss_pred cEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEE--CCCCCEEEecCHHHHHHHHHHHHHcCCceEEEE
Confidence 357888 99999999999999999999999999988779999998 5554599999999999999988752 567777
Q ss_pred E
Q 003176 104 V 104 (842)
Q Consensus 104 ~ 104 (842)
|
T Consensus 80 v 80 (81)
T smart00666 80 V 80 (81)
T ss_pred e
Confidence 6
No 8
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.74 E-value=5.3e-09 Score=71.05 Aligned_cols=27 Identities=37% Similarity=0.872 Sum_probs=25.1
Q ss_pred ccccccchhccCCchhhHHHHHHhcCC
Q 003176 724 RDCSCLVWKATGLPCHHAIAVFNSTGR 750 (842)
Q Consensus 724 ~~CsC~~~~~~GiPC~Halav~~~~~~ 750 (842)
.+|||++|+..||||+|+|+|+...++
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhCC
Confidence 479999999999999999999998875
No 9
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=98.68 E-value=8.4e-08 Score=85.71 Aligned_cols=68 Identities=13% Similarity=0.292 Sum_probs=65.0
Q ss_pred eCCHHHHHHHHHHHHHhcceeEEEEeeCccEEEEEecC------------------------------------------
Q 003176 281 FKSVIEFRDALQRFSIAHRFRYKFKKNETSRASGMCAA------------------------------------------ 318 (842)
Q Consensus 281 F~s~ee~k~ai~~yAi~~gf~~r~~ks~~~r~~~~C~~------------------------------------------ 318 (842)
|.+++|++.+|+.++...||++.+.+||.+.+.++|..
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~ki~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~k~t~srk 80 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKKKIVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKKKRTKSRK 80 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCCceEEEEEecCCCcccccccccccccccccccccccccccccccCCcccccc
Confidence 88999999999999999999999999999999999973
Q ss_pred CCCceEEEEEEeCCcceEEEEeecCCCccC
Q 003176 319 EGCSWSFYASWVPSERVFKIKKMNETHTCG 348 (842)
Q Consensus 319 ~gCpwri~as~~~~~~~w~I~~~~~~HnC~ 348 (842)
.+|||+|+|+.....+.|.|..+++.|+|+
T Consensus 81 ~~CPFriRA~yS~k~k~W~lvvvnn~HnH~ 110 (111)
T PF08731_consen 81 NTCPFRIRANYSKKNKKWTLVVVNNEHNHP 110 (111)
T ss_pred cCCCeEEEEEEEecCCeEEEEEecCCcCCC
Confidence 589999999999999999999999999996
No 10
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=98.46 E-value=8e-07 Score=77.18 Aligned_cols=74 Identities=32% Similarity=0.549 Sum_probs=58.8
Q ss_pred CeEeecCceEEEEeC-CCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccC--CceeEEEEE
Q 003176 28 SLSYDGGEANAVAIN-PETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHE--GSVTADVFV 104 (842)
Q Consensus 28 ~~~y~gg~~~~~~v~-~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~--~~~~~~v~~ 104 (842)
+++|.| +++.+.++ +++||.+|.++|++.|++....+.++| ..++..+|+|++|+||+.|++... +..+++|++
T Consensus 4 K~~~~~-~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~y--~D~e~d~v~l~sd~Dl~~a~~~~~~~~~~~l~l~v 80 (81)
T cd05992 4 KVKYGG-EIRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKY--PDEDGDLVTISSDEDLEEAIEEARRSGSKKLRLFV 80 (81)
T ss_pred EEEecC-CCEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEe--eCCCCCEEEeCCHHHHHHHHHHHhhcCCccEEEEe
Confidence 567775 56666666 999999999999999998755566666 456668999999999999999987 355677765
No 11
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=98.39 E-value=9.4e-07 Score=77.30 Aligned_cols=76 Identities=26% Similarity=0.450 Sum_probs=63.9
Q ss_pred CeEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCC--ceeEEEEEe
Q 003176 28 SLSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEG--SVTADVFVI 105 (842)
Q Consensus 28 ~~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~--~~~~~v~~~ 105 (842)
+++|.|+..+++.+++++||.+|.++|.+.|++....+.++|. .++.-+|+|++|+||..|++.... ...++++|-
T Consensus 5 K~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~--D~dgD~V~i~sd~Dl~~a~~~~~~~~~~~lrl~v~ 82 (84)
T PF00564_consen 5 KVRYGGDIRRIISLPSDVSFDDLRSKIREKFGLLDEDFQLKYK--DEDGDLVTISSDEDLQEAIEQAKESGSKTLRLFVQ 82 (84)
T ss_dssp EEEETTEEEEEEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEE--ETTSSEEEESSHHHHHHHHHHHHHCTTSCEEEEEE
T ss_pred EEEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCCCccEEEEee--CCCCCEEEeCCHHHHHHHHHHHHhcCCCcEEEEEE
Confidence 5678777777799999999999999999999987678999995 455689999999999999997642 347888875
No 12
>PF03101 FAR1: FAR1 DNA-binding domain; InterPro: IPR004330 Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. It has been found that the proteins governing this response, which include FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), are a pair of homologous proteins sharing significant sequence homology to mutator-like transposases. These proteins appear to be novel transcription factors, which are essential for activating the expression of FHY1 and FHL (for FHY1-like) and related genes, whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses in plants. The FRS (FAR1 Related Sequences) family of proteins share a similar domain structure to mutator-like transposases, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). It seems plausible that the FRS family represent transcription factors derived from mutator-like transposases [, ]. This entry represents a domain found in FAR1 and FRS proteins. It contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain.
Probab=98.31 E-value=1.4e-06 Score=77.54 Aligned_cols=59 Identities=15% Similarity=0.308 Sum_probs=52.2
Q ss_pred HHHHHHHHhcceeEEEEeeCcc-------EEEEEecC----------------------CCCceEEEEEEeCCcceEEEE
Q 003176 289 DALQRFSIAHRFRYKFKKNETS-------RASGMCAA----------------------EGCSWSFYASWVPSERVFKIK 339 (842)
Q Consensus 289 ~ai~~yAi~~gf~~r~~ks~~~-------r~~~~C~~----------------------~gCpwri~as~~~~~~~w~I~ 339 (842)
++|+.||..+||.++..++.+. ++.+.|.. +||||+|.+.+.+ ++.|.|+
T Consensus 1 ~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~-~~~w~v~ 79 (91)
T PF03101_consen 1 DFYNSYARRHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRK-DGKWRVT 79 (91)
T ss_pred CHHHHhcCcCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEcc-CCEEEEE
Confidence 4789999999999999876543 78889974 7999999999988 8899999
Q ss_pred eecCCCccC
Q 003176 340 KMNETHTCG 348 (842)
Q Consensus 340 ~~~~~HnC~ 348 (842)
.+..+|||+
T Consensus 80 ~~~~~HNH~ 88 (91)
T PF03101_consen 80 SFVLEHNHP 88 (91)
T ss_pred ECcCCcCCC
Confidence 999999997
No 13
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=98.28 E-value=3.9e-06 Score=72.64 Aligned_cols=73 Identities=26% Similarity=0.461 Sum_probs=60.2
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCC-cceEEEEecCCCCCceEeecChHHHHHHHhccC--CceeEEEEE
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEY-KSLSVKYFLPGNKQTLITICNDKDLKRMFDFHE--GSVTADVFV 104 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~-~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~--~~~~~~v~~ 104 (842)
..| ||+++.+.++.+++|.+|.+++++.|+++. +.++|||. -.| .-.++|+||+||+.-++.+. +..++++||
T Consensus 5 ~~~-~~d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~-Dde-gd~v~ltsd~DL~eai~i~~~~~~~~v~l~v 80 (82)
T cd06407 5 ATY-GEEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYL-DDD-EEWVLLTCDADLEECIDVYRSSGSHTIRLLV 80 (82)
T ss_pred EEe-CCeEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEE-CCC-CCeEEeecHHHHHHHHHHHHHCCCCeEEEEe
Confidence 344 889999999999999999999999999875 68999993 333 77899999999998766443 356788776
No 14
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=97.84 E-value=1e-05 Score=60.20 Aligned_cols=30 Identities=33% Similarity=0.754 Sum_probs=27.3
Q ss_pred eecCCccccccchhccCCchhhHHHHHHhc
Q 003176 719 VDMNKRDCSCLVWKATGLPCHHAIAVFNST 748 (842)
Q Consensus 719 V~l~~~~CsC~~~~~~GiPC~Halav~~~~ 748 (842)
+++...+|+|..|+..|.||+|++|++...
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHHHHHhh
Confidence 667889999999999999999999998764
No 15
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=97.69 E-value=0.00028 Score=62.34 Aligned_cols=75 Identities=21% Similarity=0.388 Sum_probs=61.0
Q ss_pred CeEeecCceEEEEeCC-----CCChHHHHHHHHHHhCCCC-cceEEEEecCCCCCceEeecChHHHHHHHhcc---CCce
Q 003176 28 SLSYDGGEANAVAINP-----ETHFGDLKLKLAELLNLEY-KSLSVKYFLPGNKQTLITICNDKDLKRMFDFH---EGSV 98 (842)
Q Consensus 28 ~~~y~gg~~~~~~v~~-----~~~~~~~~~~~~~~~~~~~-~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~---~~~~ 98 (842)
++.| ||++|-+.++. +++|.+|..|+.+.|+++. ..+.|+|. .++--+|++++|+||+.-++.. -...
T Consensus 4 Kv~y-~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~--Dedgd~V~l~~D~DL~~a~~~~~~~~~~~ 80 (91)
T cd06398 4 KVKY-GGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYT--DEDGDVVTLVDDNDLTDAIQYFCSGSRLN 80 (91)
T ss_pred EEEe-CCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEE--CCCCCEEEEccHHHHHHHHHHHhccCCCc
Confidence 3556 88999999985 7999999999999999987 58999993 4468899999999999988865 1234
Q ss_pred eEEEEEe
Q 003176 99 TADVFVI 105 (842)
Q Consensus 99 ~~~v~~~ 105 (842)
++||+|.
T Consensus 81 ~lrl~v~ 87 (91)
T cd06398 81 PLRIDVT 87 (91)
T ss_pred eEEEEEE
Confidence 6777764
No 16
>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA. NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is
Probab=97.68 E-value=0.00015 Score=62.77 Aligned_cols=57 Identities=23% Similarity=0.405 Sum_probs=51.5
Q ss_pred cCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhc
Q 003176 33 GGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDF 93 (842)
Q Consensus 33 gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~ 93 (842)
+|++++|.|+.+++|+||..||.++|++. +.+++||.=. ...++|++++||+.-+..
T Consensus 10 ~~Dv~~i~v~~~i~f~dL~~kIrdkf~~~-~~~~iKykDE---GD~iti~sq~DLd~Ai~~ 66 (86)
T cd06408 10 QDDTRYIMIGPDTGFADFEDKIRDKFGFK-RRLKIKMKDD---GDMITMGDQDDLDMAIDT 66 (86)
T ss_pred cCcEEEEEcCCCCCHHHHHHHHHHHhCCC-CceEEEEEcC---CCCccccCHHHHHHHHHH
Confidence 78899999999999999999999999996 6999999655 578999999999988763
No 17
>cd06405 PB1_Mekk2_3 The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development. The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, f
Probab=97.56 E-value=0.00046 Score=56.89 Aligned_cols=70 Identities=19% Similarity=0.367 Sum_probs=57.0
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCC---ceeEEEEEe
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEG---SVTADVFVI 105 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~---~~~~~v~~~ 105 (842)
++|. ||.|||-++|-+.|.|+..|+.+.|| +.+.+.|+... -||++.|-+||++-+|-.+. -..+||.+.
T Consensus 5 fE~~-gEKRIi~f~RPvkf~dl~~kv~~afG---q~mdl~ytn~e---L~iPl~~Q~DLDkAie~ld~s~~~ksLRilL~ 77 (79)
T cd06405 5 FEHN-GEKRIIQFPRPVKFKDLQQKVTTAFG---QPMDLHYTNNE---LLIPLKNQEDLDRAIELLDRSPHMKSLRILLS 77 (79)
T ss_pred EEec-CceEEEecCCCccHHHHHHHHHHHhC---CeeeEEEeccc---EEEeccCHHHHHHHHHHHccCccccceeEeEe
Confidence 3443 79999999999999999999999999 78889997544 99999999999998874443 334566553
No 18
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=97.54 E-value=0.00031 Score=59.70 Aligned_cols=65 Identities=11% Similarity=0.257 Sum_probs=55.2
Q ss_pred CeEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCC
Q 003176 28 SLSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEG 96 (842)
Q Consensus 28 ~~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~ 96 (842)
++.|.+ |-+|.|+++++|++|..||++.+.+..+.++|.|.=+.. .-++.+ +|+||+-++...-+
T Consensus 6 KV~f~~--tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkde~s-~~~v~l-~d~dle~aws~~~~ 70 (80)
T cd06406 6 KVHFKY--TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKSEAS-GEDVIL-SDTNMEDVWSQAKD 70 (80)
T ss_pred EEEEEE--EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEeccCCC-CCccCc-ChHHHHHHHHhhcC
Confidence 578887 999999999999999999999999988899999953222 456777 89999999987655
No 19
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=97.26 E-value=0.0011 Score=55.71 Aligned_cols=65 Identities=23% Similarity=0.395 Sum_probs=54.8
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCC
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEG 96 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~ 96 (842)
+.| ||+||=+..++.-+|.+|.+||...|+++..++.++|. .||.-+|++++|+||+..+.....
T Consensus 5 v~~-~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~~~~vtYi--DeD~D~ITlssd~eL~d~~~~~~~ 69 (82)
T cd06397 5 SSF-LGDTRRIVFPDIPTWEALASKLENLYNLPEIKVGVTYI--DNDNDEITLSSNKELQDFYRLSHR 69 (82)
T ss_pred EEe-CCceEEEecCCCccHHHHHHHHHHHhCCChhHeEEEEE--cCCCCEEEecchHHHHHHHHhccc
Confidence 344 56677777999999999999999999999888999994 335579999999999999886655
No 20
>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
Probab=97.08 E-value=0.0035 Score=53.36 Aligned_cols=69 Identities=22% Similarity=0.385 Sum_probs=55.4
Q ss_pred cCceEEEEeCCC-CChHHHHHHHHHHhCCCC---cceEEEEecCCCCCceEeecChHHHHHHHhccCCceeEEEEE
Q 003176 33 GGEANAVAINPE-THFGDLKLKLAELLNLEY---KSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEGSVTADVFV 104 (842)
Q Consensus 33 gg~~~~~~v~~~-~~~~~~~~~~~~~~~~~~---~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~~~~~~v~~ 104 (842)
||+.|.+.++.. ++|.||+..+...|+... .++.+||. .++..||+|++++||.--+... +.-+++||+
T Consensus 8 g~DiR~~~~~~~~~t~~~L~~~v~~~F~~~~~~~~~flIKYk--D~dGDlVTIts~~dL~~A~~~~-~~~~l~~~~ 80 (81)
T cd06401 8 GDDIRRIPIHNEDITYDELLLMMQRVFRGKLGSSDDVLIKYK--DEDGDLITIFDSSDLSFAIQCS-RILKLTLFV 80 (81)
T ss_pred CCeEEEEeccCccccHHHHHHHHHHHhccccCCcccEEEEEE--CCCCCEEEeccHHHHHHHHhcC-cceEEEEec
Confidence 999999999975 899999999999997543 48999994 4447799999999998875555 355666654
No 21
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=97.06 E-value=0.0039 Score=53.30 Aligned_cols=61 Identities=15% Similarity=0.333 Sum_probs=51.4
Q ss_pred ecCceEEEEeCCCCChHHHHHHHHHHhCCCCc-ceEEEEecCCCCCceEeecChHHHHHHHhcc
Q 003176 32 DGGEANAVAINPETHFGDLKLKLAELLNLEYK-SLSVKYFLPGNKQTLITICNDKDLKRMFDFH 94 (842)
Q Consensus 32 ~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~-~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~ 94 (842)
-+|+-.++.++.++||.+|.+|+.++|.+..+ ++++||- .|+--++++++|++|+.-+..+
T Consensus 7 y~gdi~it~~d~~~s~e~L~~~v~~~c~~~~~q~ft~kw~--DEEGDp~tiSS~~EL~EA~rl~ 68 (83)
T cd06404 7 YNGDIMITSIDPSISLEELCNEVRDMCRFHNDQPFTLKWI--DEEGDPCTISSQMELEEAFRLY 68 (83)
T ss_pred ecCcEEEEEcCCCcCHHHHHHHHHHHhCCCCCCcEEEEEE--CCCCCceeecCHHHHHHHHHHH
Confidence 47899999999999999999999999977664 8999993 3334579999999999877643
No 22
>cd06403 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The
Probab=96.92 E-value=0.0071 Score=50.98 Aligned_cols=71 Identities=17% Similarity=0.256 Sum_probs=62.4
Q ss_pred eecCceEEEEeCCC--CChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCCceeEEEEEe
Q 003176 31 YDGGEANAVAINPE--THFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEGSVTADVFVI 105 (842)
Q Consensus 31 y~gg~~~~~~v~~~--~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~~~~~~v~~~ 105 (842)
+-|+|.|=.+++|+ .||.||-+.|..+..|...+++++|+=| +--|++|+||+.+..-++-- -.-+||||-
T Consensus 6 kfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~~~f~i~Y~D~--~gDLLPInNDdNf~kAlssa--~plLRl~iq 78 (80)
T cd06403 6 KFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPNVDFLIGYTDP--HGDLLPINNDDNFLKALSSA--NPLLRIFIQ 78 (80)
T ss_pred ccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCCCcEEEEEeCC--CCCEecccCcHHHHHHHHcC--CCceEEEEE
Confidence 45899999999998 8999999999999999888999999988 56699999999999999844 346888874
No 23
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=96.83 E-value=0.0074 Score=52.66 Aligned_cols=68 Identities=19% Similarity=0.279 Sum_probs=53.8
Q ss_pred ceEEEEeCC--CCChHHHHHHHHHHh-CCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCCceeEEEEEe
Q 003176 35 EANAVAINP--ETHFGDLKLKLAELL-NLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEGSVTADVFVI 105 (842)
Q Consensus 35 ~~~~~~v~~--~~~~~~~~~~~~~~~-~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~~~~~~v~~~ 105 (842)
|-|-.+++. ++||.+|..++.++| ++....+++||. .++--||+|++|++|..-+...+ -..+||||-
T Consensus 15 EIRRf~l~~~~~~s~~~L~~~V~~~f~~l~~~~ftlky~--DeeGDlvtIssdeEL~~A~~~~~-~~~~RlyI~ 85 (87)
T cd06402 15 EIRRFAIDEDVSTSYEYLVEKVAAVFPSLRGKNFQLFWK--DEEGDLVAFSSDEELVMALGSLN-DDTFRIYIK 85 (87)
T ss_pred ceEEEEecCCCCcCHHHHHHHHHHHccccCCCcEEEEEE--CCCCCEEeecCHHHHHHHHHcCC-CCcEEEEEE
Confidence 445666644 579999999999999 554568999994 44466999999999999999875 357999874
No 24
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=96.83 E-value=0.0041 Score=53.33 Aligned_cols=69 Identities=10% Similarity=0.248 Sum_probs=55.1
Q ss_pred cCceEEEEeCC--CCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCCc-eeEEEEEe
Q 003176 33 GGEANAVAINP--ETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEGS-VTADVFVI 105 (842)
Q Consensus 33 gg~~~~~~v~~--~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~~-~~~~v~~~ 105 (842)
||++..+.++. +++|.+|.+.+.+.|+++ .+++|| |- |+.--|+|+||.||+.-++-...+ ..++++|.
T Consensus 8 ~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~--~f~lKY-lD-de~e~v~lssd~eLeE~~rl~~~~~~~l~~~v~ 79 (81)
T cd06396 8 NGESQSFLVSDSENTTWASVEAMVKVSFGLN--DIQIKY-VD-EENEEVSVNSQGEYEEALKSAVRQGNLLQMNVY 79 (81)
T ss_pred CCeEEEEEecCCCCCCHHHHHHHHHHHhCCC--cceeEE-Ec-CCCCEEEEEchhhHHHHHHHHHhCCCEEEEEEe
Confidence 78999999999 889999999999999988 899999 43 335678999999999877644332 24555553
No 25
>cd06411 PB1_p51 The PB1 domain is present in the p51 protein, a homolog of the p67 protein. p51 plays an important role in NADPH oxidase activation during phagosytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain mo
Probab=96.66 E-value=0.0074 Score=51.10 Aligned_cols=63 Identities=16% Similarity=0.228 Sum_probs=57.1
Q ss_pred ceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCCc
Q 003176 35 EANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEGS 97 (842)
Q Consensus 35 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~~ 97 (842)
=|-+|.|+|..+|++|..+|++.|.+..+..+|.|.-|+++.-|+.++.+|||+.+...-.+.
T Consensus 7 fTVai~v~~g~~y~~L~~~ls~kL~l~~~~~~LSY~~~~~~~~~v~l~~e~~me~aW~~v~~~ 69 (78)
T cd06411 7 FTVALRAPRGADVSSLRALLSQALPQQAQRGQLSYRAPGEDGHWVPISGEESLQRAWQDVADG 69 (78)
T ss_pred EEEEEEccCCCCHHHHHHHHHHHhcCChhhcEEEecCCCCCccEeecCcchHHHHHHHhccCC
Confidence 377899999999999999999999999999999999888887899999999999998866543
No 26
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=95.78 E-value=0.059 Score=46.98 Aligned_cols=71 Identities=15% Similarity=0.296 Sum_probs=57.6
Q ss_pred ecCceEEEEeCCCCChHHHHHHHHHHhCCCC---cceEEEEecCCCCCceEeecChHHHHHHHhc--cCCceeEEEEE
Q 003176 32 DGGEANAVAINPETHFGDLKLKLAELLNLEY---KSLSVKYFLPGNKQTLITICNDKDLKRMFDF--HEGSVTADVFV 104 (842)
Q Consensus 32 ~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~---~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~--~~~~~~~~v~~ 104 (842)
-.|+++=+.+..+.++.+|++.+++.+|++. +.+.|+| |-.| .-.|+++||.||..-++. ..+..+++++|
T Consensus 8 ~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~Y-lDDE-gD~VllT~D~DL~e~v~iar~~g~~~v~L~v 83 (86)
T cd06409 8 PKGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSY-VDDE-GDIVLITSDSDLVAAVLVARSAGLKKLDLHL 83 (86)
T ss_pred CCCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEE-EcCC-CCEEEEeccchHHHHHHHHHHcCCCEEEEEE
Confidence 3789999999999999999999999999987 5889999 4333 557899999999998774 34455677665
No 27
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=94.65 E-value=0.02 Score=34.66 Aligned_cols=18 Identities=28% Similarity=0.648 Sum_probs=16.3
Q ss_pred EeCCCCCcCCcCcCCCCC
Q 003176 823 VTCTKCKGIGHNKLSCKE 840 (842)
Q Consensus 823 ~~Cs~C~~~GHN~~tC~~ 840 (842)
++|-+|++.||-.+.||+
T Consensus 1 ~~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 1 RKCFNCGEPGHIARDCPK 18 (18)
T ss_dssp SBCTTTSCSSSCGCTSSS
T ss_pred CcCcCCCCcCcccccCcc
Confidence 379999999999999985
No 28
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=94.46 E-value=0.63 Score=54.17 Aligned_cols=129 Identities=12% Similarity=0.149 Sum_probs=87.7
Q ss_pred CCChhhHHHHHHHHHHhhcCCC--cEEEEecCchhHHHHHHhhcccCceEecHHHHHHHHHhhcCCCCCccccCchhHHH
Q 003176 504 TENDDSWNWFLEELRSAVSSSR--SITFVSDKQKGLMESVLKIFENAHHGYSIYHLLDNFMKNLKGPFHGEGKGSLPVNF 581 (842)
Q Consensus 504 ~Et~es~~WfL~~lk~~~~~~~--p~~iisD~~~~l~~AI~~vfP~a~h~~C~~Hi~~N~~~~~~~~~~~e~k~~~~~~~ 581 (842)
..+.+-|.-+++.+-....... -+++.+|+...+.+++. .||++.|.+..+|+.+.+.+.++.. ..+...+
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~------~~~~~~~ 307 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHD------PELKEKI 307 (470)
T ss_pred cchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhC------hHHHHHH
Confidence 5567889988888877765333 46788899999988776 9999999999999999999988642 1355666
Q ss_pred HHHHHhhhHHHHHHHHHHHHhhC---------hhHHHHHHhhccccccc--cccccCCccccccchhhhhHHHHh
Q 003176 582 LAAACAARLDSFRMSAEQVKKVS---------SNAFDWMMQIAPEYWTN--AAFKGESYQHITFDVAESYANWIE 645 (842)
Q Consensus 582 ~~~~~a~t~~eFe~~~~~l~~~~---------~~~~~yL~~~~~~~Wa~--a~f~~~~~~~~TtN~~Es~N~~lk 645 (842)
+++.+.....+++..++.+.... .++..||..+ |-. .|-. +-+.......|+.++.+.
T Consensus 308 ~~al~~~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n----~~~i~~y~~--~~~~~g~g~ee~~~~~~s 376 (470)
T PF06782_consen 308 RKALKKGDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNN----WDGIKPYRE--REGLRGIGAEESVSHVLS 376 (470)
T ss_pred HHHHHhcCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHC----HHHhhhhhh--ccCCCccchhhhhhhHHH
Confidence 67777777777777777776432 2455666654 322 1211 022233344677777663
No 29
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=93.54 E-value=0.037 Score=53.32 Aligned_cols=81 Identities=14% Similarity=0.136 Sum_probs=68.4
Q ss_pred CCeEEeccccccccccceEEEEEEecCCCCeEEEEEEEecCCChhhHHHHHHHHHHhhcCCCcEEEEecCchhHHHHHHh
Q 003176 464 RPLLFLDSTSLRSKYHEILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSSSRSITFVSDKQKGLMESVLK 543 (842)
Q Consensus 464 ~~vl~iD~T~~~~~y~~~Ll~a~g~D~~~~~~plafalv~~Et~es~~WfL~~lk~~~~~~~p~~iisD~~~~l~~AI~~ 543 (842)
++.+.+|-||.+-+=+ ..+...++|.+++ .|.+-|...-+...=..||..+.+..+ ..|..|+||+.++...|+++
T Consensus 1 ~~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~-~~p~~ivtDk~~aY~~A~~~ 76 (140)
T PF13610_consen 1 GDSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR-GEPRVIVTDKLPAYPAAIKE 76 (140)
T ss_pred CCEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec-cccceeecccCCccchhhhh
Confidence 3678999999985533 3455788999999 889999999999888999988887765 67899999999999999999
Q ss_pred hcccC
Q 003176 544 IFENA 548 (842)
Q Consensus 544 vfP~a 548 (842)
+++..
T Consensus 77 l~~~~ 81 (140)
T PF13610_consen 77 LNPEG 81 (140)
T ss_pred ccccc
Confidence 99973
No 30
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=93.19 E-value=0.14 Score=54.24 Aligned_cols=94 Identities=15% Similarity=0.176 Sum_probs=68.2
Q ss_pred EEeccccccccccceEEEEEEecC--CCCeEEEEEEEecCCChhhHHHHHHHH-HHhhcCCCcEEEEecCchhHHHHHHh
Q 003176 467 LFLDSTSLRSKYHEILLTATALDG--DDCIFPVAFAIVDTENDDSWNWFLEEL-RSAVSSSRSITFVSDKQKGLMESVLK 543 (842)
Q Consensus 467 l~iD~T~~~~~y~~~Ll~a~g~D~--~~~~~plafalv~~Et~es~~WfL~~l-k~~~~~~~p~~iisD~~~~l~~AI~~ 543 (842)
|+||=+.....++. +..+-+|. +++. -+.++++-+.++..-||..+ -.. ......+|++|...+..+||++
T Consensus 1 lgiDE~~~~~g~~~--y~t~~~d~~~~~~~---il~i~~~r~~~~l~~~~~~~~~~~-~~~~v~~V~~Dm~~~y~~~~~~ 74 (249)
T PF01610_consen 1 LGIDEFAFRKGHRS--YVTVVVDLDTDTGR---ILDILPGRDKETLKDFFRSLYPEE-ERKNVKVVSMDMSPPYRSAIRE 74 (249)
T ss_pred CeEeeeeeecCCcc--eeEEEEECccCCce---EEEEcCCccHHHHHHHHHHhCccc-cccceEEEEcCCCccccccccc
Confidence 45666655543332 33444454 3332 23588888888888888876 333 3345788999999999999999
Q ss_pred hcccCceEecHHHHHHHHHhhcC
Q 003176 544 IFENAHHGYSIYHLLDNFMKNLK 566 (842)
Q Consensus 544 vfP~a~h~~C~~Hi~~N~~~~~~ 566 (842)
.||+|.+..-.|||++++.+.+.
T Consensus 75 ~~P~A~iv~DrFHvvk~~~~al~ 97 (249)
T PF01610_consen 75 YFPNAQIVADRFHVVKLANRALD 97 (249)
T ss_pred cccccccccccchhhhhhhhcch
Confidence 99999999999999999987653
No 31
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=92.71 E-value=0.051 Score=39.82 Aligned_cols=19 Identities=32% Similarity=0.800 Sum_probs=16.5
Q ss_pred EeCCCCCcCCcCc--CCCCCC
Q 003176 823 VTCTKCKGIGHNK--LSCKET 841 (842)
Q Consensus 823 ~~Cs~C~~~GHN~--~tC~~~ 841 (842)
++|++|++.||.+ ++||.-
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~ 22 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMY 22 (40)
T ss_pred ccccccccccccccCccCCCC
Confidence 5899999999998 789863
No 32
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=89.89 E-value=0.19 Score=35.07 Aligned_cols=21 Identities=24% Similarity=0.559 Sum_probs=18.7
Q ss_pred ceEeCCCCCcCCcCcCCCCCC
Q 003176 821 RTVTCTKCKGIGHNKLSCKET 841 (842)
Q Consensus 821 r~~~Cs~C~~~GHN~~tC~~~ 841 (842)
..+.|.+|++.||..+.||..
T Consensus 7 ~~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCCEeecCCCCCccHhHCCCC
Confidence 358999999999999999974
No 33
>PF03106 WRKY: WRKY DNA -binding domain; InterPro: IPR003657 The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding []. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural studies indicate that this domain is a four-stranded beta-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure []. The WRKYGQK residues correspond to the most N-terminal beta-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the beta-sheet.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2AYD_A 1WJ2_A 2LEX_A.
Probab=89.24 E-value=0.75 Score=37.42 Aligned_cols=39 Identities=15% Similarity=0.195 Sum_probs=32.0
Q ss_pred cEEEEEecCCCCceEEEEEEeCCcceEEEEeecCCCccC
Q 003176 310 SRASGMCAAEGCSWSFYASWVPSERVFKIKKMNETHTCG 348 (842)
Q Consensus 310 ~r~~~~C~~~gCpwri~as~~~~~~~w~I~~~~~~HnC~ 348 (842)
-|..++|+..+|+++-...+..++....++++.++|||.
T Consensus 21 pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 21 PRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp EEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred eeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 466799999999999999888877788899999999996
No 34
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=88.24 E-value=4.5 Score=41.55 Aligned_cols=120 Identities=17% Similarity=0.207 Sum_probs=81.7
Q ss_pred HHHHhcCcccchhhhHHHHHHHHHhhhCCHHHHhhchHHHHHHHHHhCCCcEEEEEecCCcceeEEEEEehhhHHHHHhc
Q 003176 383 SILRDFGVTLNYSQVYRGIEGAREQLQGSYKEAYNQLPWFCDKLLEANPGSFIKLLIDNDKKFQRLFISFDASIHGFQNG 462 (842)
Q Consensus 383 ~l~~~~g~~~sy~~~~rak~~a~~~~~g~~~esy~~L~~y~~~l~~~NPg~~~~v~~d~d~~f~~lF~a~~~s~~~f~~~ 462 (842)
.+..+.|+.+.+.++.|.-++.- |.+.+.+.+.++.
T Consensus 33 e~l~~rgi~v~h~Ti~rwv~k~~--------------~~~~~~~~~r~~~------------------------------ 68 (215)
T COG3316 33 EMLAERGIEVDHETIHRWVQKYG--------------PLLARRLKRRKRK------------------------------ 68 (215)
T ss_pred HHHHHcCcchhHHHHHHHHHHHh--------------HHHHHHhhhhccc------------------------------
Confidence 34566788888888877643332 2344455555543
Q ss_pred CCCeEEeccccccccccceEEEEEEecCCCCeEEEEEEEecCCChhhHHHHHHHHHHhhcCCCcEEEEecCchhHHHHHH
Q 003176 463 CRPLLFLDSTSLRSKYHEILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSSSRSITFVSDKQKGLMESVL 542 (842)
Q Consensus 463 ~~~vl~iD~T~~~~~y~~~Ll~a~g~D~~~~~~plafalv~~Et~es~~WfL~~lk~~~~~~~p~~iisD~~~~l~~AI~ 542 (842)
-++++.+|-||.+.+-++. +.-.++|.+| .++.+-|...-+...=.-||..+++.- ..|.+|+||+.+....|+.
T Consensus 69 ~~~~w~vDEt~ikv~gkw~-ylyrAid~~g--~~Ld~~L~~rRn~~aAk~Fl~kllk~~--g~p~v~vtDka~s~~~A~~ 143 (215)
T COG3316 69 AGDSWRVDETYIKVNGKWH-YLYRAIDADG--LTLDVWLSKRRNALAAKAFLKKLLKKH--GEPRVFVTDKAPSYTAALR 143 (215)
T ss_pred cccceeeeeeEEeeccEee-ehhhhhccCC--CeEEEEEEcccCcHHHHHHHHHHHHhc--CCCceEEecCccchHHHHH
Confidence 3567788888887543332 2334556664 456677777766666667777776665 6788999999999999999
Q ss_pred hhcccCceE
Q 003176 543 KIFENAHHG 551 (842)
Q Consensus 543 ~vfP~a~h~ 551 (842)
++-+.+.|+
T Consensus 144 ~l~~~~ehr 152 (215)
T COG3316 144 KLGSEVEHR 152 (215)
T ss_pred hcCcchhee
Confidence 998866555
No 35
>PF04684 BAF1_ABF1: BAF1 / ABF1 chromatin reorganising factor; InterPro: IPR006774 ABF1 is a sequence-specific DNA binding protein involved in transcription activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on transcription and gene expression by modifying local chromatin architecture []. These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 Saccharomyces cerevisiae (P14164 from SWISSPROT)) []. The N-terminal two thirds of the protein are necessary for DNA binding, and the N terminus (amino acids 9 to 91 in S. cerevisiae) is thought to contain a novel zinc-finger motif which may stabilise the protein structure [].; GO: 0003677 DNA binding, 0006338 chromatin remodeling, 0005634 nucleus
Probab=85.36 E-value=1.7 Score=48.86 Aligned_cols=57 Identities=11% Similarity=0.332 Sum_probs=50.4
Q ss_pred CCCceeCCHHHHHHHHHHHHHhcceeEEEEeeC-ccEEEEEecCCCCceEEEEEEeCC
Q 003176 276 GVGQEFKSVIEFRDALQRFSIAHRFRYKFKKNE-TSRASGMCAAEGCSWSFYASWVPS 332 (842)
Q Consensus 276 ~vG~~F~s~ee~k~ai~~yAi~~gf~~r~~ks~-~~r~~~~C~~~gCpwri~as~~~~ 332 (842)
.-+..|+++++-+.+|+.|-...++.|..+.|- .+.|++.|....|||+|..+....
T Consensus 23 ~~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nkhftfachlk~c~fkillsy~g~ 80 (496)
T PF04684_consen 23 AQARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNKHFTFACHLKNCPFKILLSYCGN 80 (496)
T ss_pred ccccCCCcHHHHHHHHhhhhhhhcCceeecccccccceEEEeeccCCCceeeeeeccc
Confidence 457789999999999999999999999998774 467999999999999999987653
No 36
>PF04500 FLYWCH: FLYWCH zinc finger domain; InterPro: IPR007588 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a potential FLYWCH Zn-finger domain found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH where X indicates any amino acid. This domain was first characterised in Drosophila Modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs []. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain. FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione SH-transferase (GST) domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2RPR_A.
Probab=85.35 E-value=1.5 Score=35.18 Aligned_cols=46 Identities=20% Similarity=0.429 Sum_probs=25.2
Q ss_pred cceeEEEEeeCccEEEEEecC---CCCceEEEEEEeCCcceEEEEeecCCCcc
Q 003176 298 HRFRYKFKKNETSRASGMCAA---EGCSWSFYASWVPSERVFKIKKMNETHTC 347 (842)
Q Consensus 298 ~gf~~r~~ks~~~r~~~~C~~---~gCpwri~as~~~~~~~w~I~~~~~~HnC 347 (842)
.|+.|...+.........|.. .+|+++|... .+ .-.|.....+|||
T Consensus 14 ~Gy~y~~~~~~~~~~~WrC~~~~~~~C~a~~~~~--~~--~~~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRNDGKTYWRCSRRRSHGCRARLITD--AG--DGRVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-SS-EEEEEGGGTTS----EEEEE------TTEEEE-S---SS
T ss_pred CCeEEECcCCCCCcEEEEeCCCCCCCCeEEEEEE--CC--CCEEEECCCccCC
Confidence 578888877778889999985 3899999987 22 2345555688987
No 37
>cd06399 PB1_P40 The PB1 domain is essential part of the p40 adaptor protein which plays an important role in activating phagocyte NADPH oxidase during phagocytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes , such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domain of p40 represents a type I PB1 domain which interacts with the PB1 domain of oxidase activator p67 w
Probab=84.92 E-value=3 Score=36.05 Aligned_cols=60 Identities=17% Similarity=0.224 Sum_probs=49.2
Q ss_pred cCceEEEEeCCCC----ChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCC
Q 003176 33 GGEANAVAINPET----HFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEG 96 (842)
Q Consensus 33 gg~~~~~~v~~~~----~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~ 96 (842)
|-.+|=|.|..++ +|.||...+...|+ .+.+.|-|+=+..| ||-|-+|||+.=|++...+
T Consensus 12 ~~~~rdi~vee~l~~~P~~kdLl~lmr~~f~--~~dIaLNYrD~EGD--LIRllddeDv~LMV~~~r~ 75 (92)
T cd06399 12 ISTIRDIAVEEDLSSTPLLKDLLELTRREFQ--REDIALNYRDAEGD--LIRLLSDEDVALMVRQSRG 75 (92)
T ss_pred CccccceEeecccccCccHHHHHHHHHHHhc--hhheeeeeecCCCC--EEEEcchhhHHHHHHHHhc
Confidence 5567778887775 79999999999997 45899999855443 9999999999999997754
No 38
>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.
Probab=84.23 E-value=3.1 Score=35.48 Aligned_cols=38 Identities=11% Similarity=-0.006 Sum_probs=35.0
Q ss_pred ecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 32 DGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 32 ~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
.+|.|..|.|+.++|-.+++.||.+..|++.+...| |.
T Consensus 10 ~~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~ 47 (75)
T cd01799 10 SHTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VI 47 (75)
T ss_pred cCCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-Ec
Confidence 478999999999999999999999999999998888 64
No 39
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=83.08 E-value=6.1 Score=36.10 Aligned_cols=76 Identities=11% Similarity=0.020 Sum_probs=57.5
Q ss_pred CCCeEEecccccc-ccccceEEEEEEecCCCCeEEEEEEEecCCChhhHHHHHHHHHHhhcCCCcEEEEecCchhHHH
Q 003176 463 CRPLLFLDSTSLR-SKYHEILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSSSRSITFVSDKQKGLME 539 (842)
Q Consensus 463 ~~~vl~iD~T~~~-~~y~~~Ll~a~g~D~~~~~~plafalv~~Et~es~~WfL~~lk~~~~~~~p~~iisD~~~~l~~ 539 (842)
-...+.+|.++.. ...++.....+.+|..-.. .+++.+-..++.+.+..+|+......+...|.+|++|+..+..+
T Consensus 5 p~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~p~~i~tD~g~~f~~ 81 (120)
T PF00665_consen 5 PGERWQIDFTPMPIPDKGGRVYLLVFIDDYSRF-IYAFPVSSKETAEAALRALKRAIEKRGGRPPRVIRTDNGSEFTS 81 (120)
T ss_dssp TTTEEEEEEEEETGGCTT-CEEEEEEEETTTTE-EEEEEESSSSHHHHHHHHHHHHHHHHS-SE-SEEEEESCHHHHS
T ss_pred CCCEEEEeeEEEecCCCCccEEEEEEEECCCCc-EEEEEeecccccccccccccccccccccccceeccccccccccc
Confidence 3568899999666 3455588888999976654 55777777788888888888877777766699999999998864
No 40
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=82.59 E-value=2.3 Score=35.73 Aligned_cols=38 Identities=8% Similarity=0.151 Sum_probs=35.9
Q ss_pred cCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 33 GGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 33 gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
||++..+.|+.++|.++|+.+|++..|++.+...|-|.
T Consensus 8 ~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li~~ 45 (71)
T cd01796 8 SETTFSLDVDPDLELENFKALCEAESGIPASQQQLIYN 45 (71)
T ss_pred CCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEEEEC
Confidence 89999999999999999999999999999988888885
No 41
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=81.37 E-value=3.3 Score=34.99 Aligned_cols=42 Identities=14% Similarity=0.199 Sum_probs=38.1
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
++..+|++..+.|+.+.|-.+|+++|++..|++.+...|-|.
T Consensus 5 vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~ 46 (74)
T cd01807 5 VKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFK 46 (74)
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEEC
Confidence 467789999999999999999999999999999988888774
No 42
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=81.35 E-value=2.9 Score=34.70 Aligned_cols=41 Identities=29% Similarity=0.513 Sum_probs=37.0
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
++| ||++.-+.|+.+.|-.+|+++|++..+++.+...|.|.
T Consensus 5 vk~-~g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~ 45 (71)
T cd01812 5 VKH-GGESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFK 45 (71)
T ss_pred EEE-CCEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeC
Confidence 567 49999999999999999999999999999988888875
No 43
>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins. SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....
Probab=81.10 E-value=3.7 Score=34.31 Aligned_cols=41 Identities=17% Similarity=0.263 Sum_probs=38.1
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCC-cceEEEE
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEY-KSLSVKY 69 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~-~~~~~~y 69 (842)
|+-.+|+.--+.|.++.+++.|+.+.++..|++. +.+.|.|
T Consensus 5 v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~f 46 (72)
T PF11976_consen 5 VRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIF 46 (72)
T ss_dssp EEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEE
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEE
Confidence 6677899999999999999999999999999999 8888888
No 44
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=80.68 E-value=2.8 Score=36.67 Aligned_cols=46 Identities=13% Similarity=0.182 Sum_probs=34.8
Q ss_pred EEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecCh
Q 003176 39 VAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICND 84 (842)
Q Consensus 39 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d 84 (842)
+.++.+|+.+||+.||...+|++.+.+.|.|.=..++..+..+.+|
T Consensus 18 kr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd 63 (87)
T PF14560_consen 18 KRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDD 63 (87)
T ss_dssp EEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGS
T ss_pred EEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCC
Confidence 6789999999999999999999999999988423333555555333
No 45
>PHA02517 putative transposase OrfB; Reviewed
Probab=80.43 E-value=17 Score=39.06 Aligned_cols=152 Identities=17% Similarity=0.118 Sum_probs=85.2
Q ss_pred hhHHHHHhHhhc-CCCCChhHHHHHHHHhcCcccchhhhHHHHHHHHHhhhCCHHHHhhchHHHHHHHHHhCCCcEEEEE
Q 003176 360 WLVSIIKDKLRE-SPHHKPKEISKSILRDFGVTLNYSQVYRGIEGAREQLQGSYKEAYNQLPWFCDKLLEANPGSFIKLL 438 (842)
Q Consensus 360 ~ia~~~~~~l~~-~~~~~~~~I~~~l~~~~g~~~sy~~~~rak~~a~~~~~g~~~esy~~L~~y~~~l~~~NPg~~~~v~ 438 (842)
.+.+.+.+.+.. .+.+..+.|...|.++ |+.++.++++|....+ |-... .. ..-.....+-. .
T Consensus 30 ~l~~~I~~i~~~~~~~~G~r~I~~~L~~~-g~~vs~~tV~Rim~~~-----gl~~~-~~------~k~~~~~~~~~---~ 93 (277)
T PHA02517 30 WLKSEILRVYDENHQVYGVRKVWRQLNRE-GIRVARCTVGRLMKEL-----GLAGV-LR------GKKVRTTISRK---A 93 (277)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHhc-CcccCHHHHHHHHHHc-----CCceE-ec------CCCcCCCCCCC---C
Confidence 455666666654 5788999999988765 9999999998764321 10000 00 00000000000 0
Q ss_pred ecCCcceeEEEEEehhhHHHHHhcCCCeEEeccccccccccceEEEEEEecCCCCeEEEEEEEecCCChhhHHHHHHHHH
Q 003176 439 IDNDKKFQRLFISFDASIHGFQNGCRPLLFLDSTSLRSKYHEILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELR 518 (842)
Q Consensus 439 ~d~d~~f~~lF~a~~~s~~~f~~~~~~vl~iD~T~~~~~y~~~Ll~a~g~D~~~~~~plafalv~~Et~es~~WfL~~lk 518 (842)
....+.+.+-|-+. .-..++..|.||..... +..++++.+|...+ +++|+.+...++.+...-+|+...
T Consensus 94 ~~~~n~~~r~f~~~---------~pn~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~~~~l~~a~ 162 (277)
T PHA02517 94 VAAPDRVNRQFVAT---------RPNQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDFVLDALEQAL 162 (277)
T ss_pred CCCCCcccCCCCCC---------CCCCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHHHHHHHHHHH
Confidence 00011111212111 13468999999987554 45667777776654 567888888888776555555444
Q ss_pred HhhcCCCcEEEEecCchhHH
Q 003176 519 SAVSSSRSITFVSDKQKGLM 538 (842)
Q Consensus 519 ~~~~~~~p~~iisD~~~~l~ 538 (842)
...+...+..|.||+.....
T Consensus 163 ~~~~~~~~~i~~sD~G~~y~ 182 (277)
T PHA02517 163 WARGRPGGLIHHSDKGSQYV 182 (277)
T ss_pred HhcCCCcCcEeecccccccc
Confidence 44443344677899987654
No 46
>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein. Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
Probab=79.92 E-value=4.2 Score=33.79 Aligned_cols=41 Identities=20% Similarity=0.262 Sum_probs=37.4
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEE
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKY 69 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y 69 (842)
++...|++..+.|+.+.+-.+|++++++..|++.+...|-|
T Consensus 5 vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~ 45 (72)
T cd01809 5 VKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIY 45 (72)
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEE
Confidence 45678899999999999999999999999999988888888
No 47
>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein. DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.
Probab=79.53 E-value=3.6 Score=34.48 Aligned_cols=43 Identities=12% Similarity=0.172 Sum_probs=39.1
Q ss_pred CeEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 28 SLSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 28 ~~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
+++..+|++..+.|+.+.|-.+++++|++..|++.....|-|.
T Consensus 2 ~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~ 44 (70)
T cd01794 2 KVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFS 44 (70)
T ss_pred eEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEEC
Confidence 4678899999999999999999999999999999888888774
No 48
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=78.99 E-value=49 Score=35.39 Aligned_cols=145 Identities=17% Similarity=0.103 Sum_probs=87.4
Q ss_pred chhhHHHHHhHhhcCCCCChhHHHHHHHHh---cCc-ccchhhhHHHHHHH-HHhhhCCHHHHhhchHHHHHHHHHhCCC
Q 003176 358 KNWLVSIIKDKLRESPHHKPKEISKSILRD---FGV-TLNYSQVYRGIEGA-REQLQGSYKEAYNQLPWFCDKLLEANPG 432 (842)
Q Consensus 358 ~~~ia~~~~~~l~~~~~~~~~~I~~~l~~~---~g~-~~sy~~~~rak~~a-~~~~~g~~~esy~~L~~y~~~l~~~NPg 432 (842)
...+...+++.+...+.+..+.|...|+++ .|+ .++...++|....+ +.... +...+.
T Consensus 10 ~~~l~~~I~~~~~~~~~yG~rri~~~L~~~~~~~g~~~v~~krV~rlmr~~gL~~~~-----------------r~~~~~ 72 (262)
T PRK14702 10 DTDVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRLMRQNALLLER-----------------KPAVPP 72 (262)
T ss_pred hHHHHHHHHHHHHhCcccChHHHHHHHHhhhcccCccccCHHHHHHHHHHhCCcccc-----------------CCCCCC
Confidence 344556677766777889999999988875 477 48988888764332 11000 000000
Q ss_pred cEEEEEecCCcceeEEEEEehhhHHHHHhcCCCeEEeccccccccccceEEEEEEecCCCCeEEEEEEEecC-CChhhHH
Q 003176 433 SFIKLLIDNDKKFQRLFISFDASIHGFQNGCRPLLFLDSTSLRSKYHEILLTATALDGDDCIFPVAFAIVDT-ENDDSWN 511 (842)
Q Consensus 433 ~~~~v~~d~d~~f~~lF~a~~~s~~~f~~~~~~vl~iD~T~~~~~y~~~Ll~a~g~D~~~~~~plafalv~~-Et~es~~ 511 (842)
+. . +.... |. ...-..++..|-||.....++.++.++-+|.... .+||+++... -+.+.-.
T Consensus 73 ~~------~-~~~~~-~~---------~~~pn~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~ 134 (262)
T PRK14702 73 SK------R-AHTGR-VA---------VKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQ 134 (262)
T ss_pred CC------c-CCCCc-cc---------cCCCCCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHH
Confidence 00 0 00000 10 1113468999999987655557888888997776 7889999874 5666665
Q ss_pred HHHHHHHHhh-c---CCCcEEEEecCchhH
Q 003176 512 WFLEELRSAV-S---SSRSITFVSDKQKGL 537 (842)
Q Consensus 512 WfL~~lk~~~-~---~~~p~~iisD~~~~l 537 (842)
-+|+...+.. + ...|..|.||+....
T Consensus 135 ~~l~~A~~~~~~~~~~~~~~iihSD~Gsqy 164 (262)
T PRK14702 135 DVMLGAVERRFGNDLPSSPVEWLTDNGSCY 164 (262)
T ss_pred HHHHHHHHHHhcccCCCCCeEEEcCCCccc
Confidence 6666444332 2 235788899987654
No 49
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=78.93 E-value=4.1 Score=33.91 Aligned_cols=42 Identities=21% Similarity=0.317 Sum_probs=38.2
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
++..+|++..+.|+.+.|..+++++|++..|++.+...|-|.
T Consensus 3 vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li~~ 44 (70)
T cd01798 3 VRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFA 44 (70)
T ss_pred EEcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEEEC
Confidence 456789999999999999999999999999999998888775
No 50
>PF03050 DDE_Tnp_IS66: Transposase IS66 family ; InterPro: IPR004291 Transposase proteins are necessary for efficient DNA transposition. This family includes the bacterial insertion sequence (IS) element, IS66, from Agrobacterium tumefaciens []. IS66 may cause genetic and structural variations of the T region and the vir region of the octopine Ti plasmids []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=78.71 E-value=3.5 Score=44.25 Aligned_cols=133 Identities=21% Similarity=0.235 Sum_probs=82.2
Q ss_pred CCCChhHHHHHHHHhcCcccchhhhHHHHHHHHHhhhCCHHHHhhchHHHHHHHHHhCCCcEEEEEecCCcceeEEEEEe
Q 003176 373 PHHKPKEISKSILRDFGVTLNYSQVYRGIEGAREQLQGSYKEAYNQLPWFCDKLLEANPGSFIKLLIDNDKKFQRLFISF 452 (842)
Q Consensus 373 ~~~~~~~I~~~l~~~~g~~~sy~~~~rak~~a~~~~~g~~~esy~~L~~y~~~l~~~NPg~~~~v~~d~d~~f~~lF~a~ 452 (842)
..++...+.+.+.+. |+.+|...+.+.....-+.+.. .| +.+.+.
T Consensus 19 ~~lp~~r~~~~~~~~-G~~is~~ti~~~~~~~~~~l~~----~~-------~~l~~~----------------------- 63 (271)
T PF03050_consen 19 YHLPLYRIQQMLEDL-GITISRGTIANWIKRVAEALKP----LY-------EALKEE----------------------- 63 (271)
T ss_pred CCCCHHHHhhhhhcc-ceeeccchhHhHhhhhhhhhhh----hh-------hhhhhh-----------------------
Confidence 445556666666666 9999999888765555433211 11 122221
Q ss_pred hhhHHHHHhcCCCeEEecccccc----ccccc-eEEEEEEecCCCCeEEEEEEEecCCChhhHHHHHHHHHHhhcCCCcE
Q 003176 453 DASIHGFQNGCRPLLFLDSTSLR----SKYHE-ILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSSSRSI 527 (842)
Q Consensus 453 ~~s~~~f~~~~~~vl~iD~T~~~----~~y~~-~Ll~a~g~D~~~~~~plafalv~~Et~es~~WfL~~lk~~~~~~~p~ 527 (842)
.. -.+++.+|-|..+ ++... -+-++++-+ .+.|.+.++=..+...-+|.. -.-
T Consensus 64 -------~~-~~~~~~~DET~~~vl~~~~g~~~~~Wv~~~~~------~v~f~~~~sR~~~~~~~~L~~--------~~G 121 (271)
T PF03050_consen 64 -------LR-SSPVVHADETGWRVLDKGKGKKGYLWVFVSPE------VVLFFYAPSRSSKVIKEFLGD--------FSG 121 (271)
T ss_pred -------cc-ccceeccCCceEEEeccccccceEEEeeeccc------eeeeeecccccccchhhhhcc--------cce
Confidence 11 3578888888777 44332 233333322 556666666666555555433 224
Q ss_pred EEEecCchhHHHHHHhhcccCceEecHHHHHHHHHhhcCC
Q 003176 528 TFVSDKQKGLMESVLKIFENAHHGYSIYHLLDNFMKNLKG 567 (842)
Q Consensus 528 ~iisD~~~~l~~AI~~vfP~a~h~~C~~Hi~~N~~~~~~~ 567 (842)
+++||+-.+-.. +....|+.|+.|+.|.|.+....
T Consensus 122 ilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~~ 156 (271)
T PF03050_consen 122 ILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAES 156 (271)
T ss_pred eeeccccccccc-----ccccccccccccccccccccccc
Confidence 899999988754 33889999999999999887654
No 51
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=77.76 E-value=4.6 Score=33.93 Aligned_cols=41 Identities=10% Similarity=0.225 Sum_probs=37.2
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEE
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKY 69 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y 69 (842)
++..+|++..+.|+.+.|-.+|+.+|++..+++.+.+.|.|
T Consensus 5 v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~ 45 (76)
T cd01803 5 VKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 45 (76)
T ss_pred EEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEE
Confidence 45667999999999999999999999999999988888887
No 52
>cd00196 UBQ Ubiquitin-like proteins. Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate.
Probab=77.41 E-value=5.3 Score=30.77 Aligned_cols=47 Identities=21% Similarity=0.145 Sum_probs=38.9
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCC
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNK 75 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~ 75 (842)
+.+.||.+..+.++.++|..+|++++++.++.+.+.+.|-|.-+..+
T Consensus 2 v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~~~~~ 48 (69)
T cd00196 2 VKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILP 48 (69)
T ss_pred eEecCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECCeECC
Confidence 34558999999999999999999999999998878888877654433
No 53
>smart00774 WRKY DNA binding domain. The WRKY domain is a DNA binding domain found in one or two copies in a superfamily of plant transcription factors. These transcription factors are involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence and trichome development. The domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger-like motif. It binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core is essential for function and WRKY binding.
Probab=77.39 E-value=3.2 Score=33.57 Aligned_cols=38 Identities=16% Similarity=0.174 Sum_probs=30.5
Q ss_pred cEEEEEecC-CCCceEEEEEEeCCcceEEEEeecCCCcc
Q 003176 310 SRASGMCAA-EGCSWSFYASWVPSERVFKIKKMNETHTC 347 (842)
Q Consensus 310 ~r~~~~C~~-~gCpwri~as~~~~~~~w~I~~~~~~HnC 347 (842)
-|...+|+. .||+++=.+.+..++....+.++.++|||
T Consensus 21 pRsYYrCt~~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 21 PRSYYRCTYSQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred cceEEeccccCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 356689998 89999877777765556677889999998
No 54
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=75.96 E-value=66 Score=35.18 Aligned_cols=143 Identities=17% Similarity=0.124 Sum_probs=86.0
Q ss_pred hhHHHHHhHhhcCCCCChhHHHHHHHHhc---Cc-ccchhhhHHHHHHH-HHhhhCCHHHHhhchHHHHHHHHHhCCCcE
Q 003176 360 WLVSIIKDKLRESPHHKPKEISKSILRDF---GV-TLNYSQVYRGIEGA-REQLQGSYKEAYNQLPWFCDKLLEANPGSF 434 (842)
Q Consensus 360 ~ia~~~~~~l~~~~~~~~~~I~~~l~~~~---g~-~~sy~~~~rak~~a-~~~~~g~~~esy~~L~~y~~~l~~~NPg~~ 434 (842)
.+...|++.....+.+..+.|...|+++. |+ .++..+++|..+.+ +.... +...+.+.
T Consensus 51 ~l~~~I~~i~~~~~~yG~Rri~~~L~~~g~~~g~~~v~~k~V~RlMr~~Gl~~~~-----------------~~~~~~~~ 113 (301)
T PRK09409 51 DVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRIMRQNALLLER-----------------KPAVPPSK 113 (301)
T ss_pred HHHHHHHHHHHhCccCCHHHHHHHHHhhhcccCccccCHHHHHHHHHHcCCcccc-----------------cCCCCCCC
Confidence 45556666666678899999999887752 66 58888888753322 10000 00000000
Q ss_pred EEEEecCCcceeEEEEEehhhHHHHHhcCCCeEEeccccccccccceEEEEEEecCCCCeEEEEEEEecC-CChhhHHHH
Q 003176 435 IKLLIDNDKKFQRLFISFDASIHGFQNGCRPLLFLDSTSLRSKYHEILLTATALDGDDCIFPVAFAIVDT-ENDDSWNWF 513 (842)
Q Consensus 435 ~~v~~d~d~~f~~lF~a~~~s~~~f~~~~~~vl~iD~T~~~~~y~~~Ll~a~g~D~~~~~~plafalv~~-Et~es~~Wf 513 (842)
...... |. ...-..++..|-||....-++.++.++-+|.... .+||+++... .+.+.-.-+
T Consensus 114 -------~~~~~~-~~---------~~~pN~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~ 175 (301)
T PRK09409 114 -------RAHTGR-VA---------VKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDV 175 (301)
T ss_pred -------CCCCCC-cC---------CCCCCCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHH
Confidence 000000 10 1113469999999987655556888888998776 7889999876 566666666
Q ss_pred HHH-HHHhhcC---CCcEEEEecCchhH
Q 003176 514 LEE-LRSAVSS---SRSITFVSDKQKGL 537 (842)
Q Consensus 514 L~~-lk~~~~~---~~p~~iisD~~~~l 537 (842)
|+. +..+.+. ..|..|-||+....
T Consensus 176 l~~a~~~~~~~~~~~~~~iihSDrGsqy 203 (301)
T PRK09409 176 MLGAVERRFGNDLPSSPVEWLTDNGSCY 203 (301)
T ss_pred HHHHHHHHhccCCCCCCcEEecCCCccc
Confidence 654 3333332 24678899987654
No 55
>PTZ00044 ubiquitin; Provisional
Probab=75.35 E-value=6.3 Score=33.27 Aligned_cols=42 Identities=17% Similarity=0.340 Sum_probs=37.9
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
++-..|++..+.|+.+.|=.+|+++|++..|++.+...|-|.
T Consensus 5 vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~ 46 (76)
T PTZ00044 5 IKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYS 46 (76)
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEEC
Confidence 455689999999999999999999999999999998888884
No 56
>PF13565 HTH_32: Homeodomain-like domain
Probab=74.18 E-value=4.9 Score=33.98 Aligned_cols=41 Identities=29% Similarity=0.469 Sum_probs=34.3
Q ss_pred hhHHHHHhHhhcCCCCChhHHHHHHHHhcCccc--chhhhHHH
Q 003176 360 WLVSIIKDKLRESPHHKPKEISKSILRDFGVTL--NYSQVYRG 400 (842)
Q Consensus 360 ~ia~~~~~~l~~~~~~~~~~I~~~l~~~~g~~~--sy~~~~ra 400 (842)
.+...+.+.+..+|.+++.+|...|.+++|+.+ |++.+||.
T Consensus 34 e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 34 EQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 344566777778899999999999999999876 99999874
No 57
>smart00343 ZnF_C2HC zinc finger.
Probab=74.07 E-value=1.6 Score=28.95 Aligned_cols=17 Identities=29% Similarity=0.724 Sum_probs=15.2
Q ss_pred eCCCCCcCCcCcCCCCC
Q 003176 824 TCTKCKGIGHNKLSCKE 840 (842)
Q Consensus 824 ~Cs~C~~~GHN~~tC~~ 840 (842)
.|.+|++.||..+.||.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 48999999999999983
No 58
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=73.24 E-value=1.3 Score=34.39 Aligned_cols=19 Identities=32% Similarity=0.761 Sum_probs=17.1
Q ss_pred eEeCCCCCcCCcCcCCCCC
Q 003176 822 TVTCTKCKGIGHNKLSCKE 840 (842)
Q Consensus 822 ~~~Cs~C~~~GHN~~tC~~ 840 (842)
...|.+|+..||..+.||.
T Consensus 31 p~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred ChhhcCCCCcCcCHhHcCC
Confidence 4689999999999999983
No 59
>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120. SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.
Probab=72.07 E-value=6.9 Score=33.25 Aligned_cols=39 Identities=15% Similarity=0.158 Sum_probs=36.3
Q ss_pred ecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 32 DGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 32 ~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
.+|++..+.|+.++|-.+|+.+|.+..+++.+...|.|.
T Consensus 5 l~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~ 43 (76)
T cd01800 5 LNGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYE 43 (76)
T ss_pred cCCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEEC
Confidence 479999999999999999999999999999998899885
No 60
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=71.79 E-value=55 Score=32.00 Aligned_cols=63 Identities=10% Similarity=0.175 Sum_probs=49.9
Q ss_pred CChhhHHHHHHHHHHhhcCCCcEEEEecCchhHHHHHH---hhcccCceEecHHHHHHHHHhhcCC
Q 003176 505 ENDDSWNWFLEELRSAVSSSRSITFVSDKQKGLMESVL---KIFENAHHGYSIYHLLDNFMKNLKG 567 (842)
Q Consensus 505 Et~es~~WfL~~lk~~~~~~~p~~iisD~~~~l~~AI~---~vfP~a~h~~C~~Hi~~N~~~~~~~ 567 (842)
.+.+...-+|+...+.+|..+-.-||||....+.+|-+ +-+|.....-|.-|-+.-+.+.+..
T Consensus 73 ~~a~~l~~ll~~vIeeVG~~nVvqVVTDn~~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 73 KTAEYLFELLDEVIEEVGEENVVQVVTDNASNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred ccHHHHHHHHHHHHHHhhhhhhhHHhccCchhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 46667777777777777877777799999999888844 4489999999999999888777653
No 61
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=71.49 E-value=9.8 Score=31.88 Aligned_cols=42 Identities=14% Similarity=0.203 Sum_probs=36.9
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
++-.+|++..+.|+.+.|-++|+.+|++..+++.+.+.|-|.
T Consensus 5 v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~ 46 (76)
T cd01806 5 VKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYS 46 (76)
T ss_pred EEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEEC
Confidence 345578888899999999999999999999999998888874
No 62
>cd01763 Sumo Small ubiquitin-related modifier (SUMO). Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
Probab=69.84 E-value=9.1 Score=33.52 Aligned_cols=45 Identities=13% Similarity=0.090 Sum_probs=40.2
Q ss_pred CCCeEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 26 DGSLSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 26 ~~~~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
.-.+...-|.+..+.|.++.+++.++.++++..|++.+.+.|-|.
T Consensus 13 ~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~ 57 (87)
T cd01763 13 NLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFD 57 (87)
T ss_pred EEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEEC
Confidence 345677789999999999999999999999999999999999884
No 63
>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.
Probab=69.28 E-value=7.6 Score=32.15 Aligned_cols=39 Identities=15% Similarity=0.124 Sum_probs=27.7
Q ss_pred ecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 32 DGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 32 ~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
-+|++.-|.|.++++..+...+.|+.++++.+...|+|+
T Consensus 4 ~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~ 42 (65)
T PF11470_consen 4 YNFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHN 42 (65)
T ss_dssp TTS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEET
T ss_pred cCCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEEC
Confidence 367888899999999999999999999999986666663
No 64
>cd01805 RAD23_N Ubiquitin-like domain of RAD23. RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=69.19 E-value=12 Score=31.65 Aligned_cols=42 Identities=14% Similarity=0.195 Sum_probs=37.0
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCC--CCcceEEEEe
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNL--EYKSLSVKYF 70 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~--~~~~~~~~y~ 70 (842)
++..+|++..+.|+.+.|-.+|+.+|++..++ +.+...|-|.
T Consensus 5 vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~ 48 (77)
T cd01805 5 FKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYS 48 (77)
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEEC
Confidence 56789999999999999999999999999998 7777777763
No 65
>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=68.83 E-value=10 Score=32.00 Aligned_cols=42 Identities=10% Similarity=0.188 Sum_probs=37.5
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
++...|++..+.|+.+.|-.+++++|++..|++.+...|-|.
T Consensus 3 vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~~ 44 (74)
T cd01810 3 VRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFE 44 (74)
T ss_pred EECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEEC
Confidence 466789999999999999999999999999999888888763
No 66
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=68.55 E-value=9.1 Score=34.27 Aligned_cols=29 Identities=28% Similarity=0.632 Sum_probs=22.2
Q ss_pred CceeEeecCCccccccchh----ccC-CchhhHHHH
Q 003176 714 DSTHVVDMNKRDCSCLVWK----ATG-LPCHHAIAV 744 (842)
Q Consensus 714 ~~~~~V~l~~~~CsC~~~~----~~G-iPC~Halav 744 (842)
++.|+++.+ .|||..|- ..| -||.|++.+
T Consensus 42 ~rdYIl~~g--fCSCp~~~~svvl~Gk~~C~Hi~gl 75 (117)
T COG5431 42 ERDYILEGG--FCSCPDFLGSVVLKGKSPCAHIIGL 75 (117)
T ss_pred ccceEEEcC--cccCHHHHhHhhhcCcccchhhhhe
Confidence 457888877 99999886 333 679999974
No 67
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=67.89 E-value=13 Score=30.19 Aligned_cols=41 Identities=17% Similarity=0.249 Sum_probs=35.5
Q ss_pred EeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 30 SYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 30 ~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
+..+|.+..+.++.++|..+|+.++++.++++.+.+.|.|.
T Consensus 3 ~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~ 43 (69)
T cd01769 3 KTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYA 43 (69)
T ss_pred EccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEEC
Confidence 44567788889999999999999999999999888888774
No 68
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=66.65 E-value=13 Score=29.60 Aligned_cols=41 Identities=20% Similarity=0.283 Sum_probs=34.2
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
++..+ .+..+.|+.+.+..+|+.+|++.++++.+.+.|.|.
T Consensus 5 vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~ 45 (64)
T smart00213 5 VKTLD-GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYK 45 (64)
T ss_pred EEECC-ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEEC
Confidence 34455 577899999999999999999999998887777764
No 69
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=66.58 E-value=13 Score=32.39 Aligned_cols=47 Identities=17% Similarity=0.280 Sum_probs=34.5
Q ss_pred EEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHH
Q 003176 39 VAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKD 86 (842)
Q Consensus 39 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~d 86 (842)
..++.+|+.++|+.||...+|+++..+.|.|. .+++..+..+.+|+.
T Consensus 17 kr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~-~~~~~~~~~l~~d~~ 63 (84)
T cd01789 17 KKYSRGLTIAELKKKLELVVGTPASSMRLQLF-DGDDKLVSKLDDDDA 63 (84)
T ss_pred EecCCCCcHHHHHHHHHHHHCCCccceEEEEE-cCCCCeEeecCCCcc
Confidence 34899999999999999999999999999763 333333333444443
No 70
>cd06395 PB1_Map2k5 PB1 domain is essential part of the mitogen-activated protein kinase kinase 5 (Map2k5, alias MEK5) one of the key member of the signaling kinases cascade which involved in angiogenesis and early cardiovascular development. The PB1 domain of Map2k5 interacts with the PB1 domain of another members of kinase cascade MEKK2 (or MEKK3). A canonical PB1-PB1 interaction, involving heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The Map2k5 protein contains a type I PB1 domain.
Probab=65.93 E-value=13 Score=31.63 Aligned_cols=49 Identities=22% Similarity=0.426 Sum_probs=38.9
Q ss_pred CCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhcc
Q 003176 43 PETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFH 94 (842)
Q Consensus 43 ~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~ 94 (842)
..++|.|+..-|...+. +...-.|.| ..|+.-=|+|.+||.|+.|+..+
T Consensus 21 ~~L~F~DvL~~I~~vlp-~aT~tAFeY--EDE~gDRITVRSDeEm~AMlsyy 69 (91)
T cd06395 21 PQLLFRDVLDVIGQVLP-EATTTAFEY--EDEDGDRITVRSDEEMKAMLSYY 69 (91)
T ss_pred ccccHHHHHHHHHHhcc-cccccceee--ccccCCeeEecchHHHHHHHHHH
Confidence 56899999999999994 223455666 56666679999999999999844
No 71
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=63.42 E-value=16 Score=30.74 Aligned_cols=40 Identities=10% Similarity=0.194 Sum_probs=36.1
Q ss_pred eecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 31 YDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 31 y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
-.|+++..+.|+.+.|-++++.+|++..|++.+...|-|.
T Consensus 5 vk~~~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~ 44 (74)
T cd01793 5 VRAQNTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLA 44 (74)
T ss_pred EECCCEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEEC
Confidence 3467899999999999999999999999999988888885
No 72
>cd01813 UBP_N UBP ubiquitin processing protease. The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.
Probab=61.78 E-value=18 Score=30.59 Aligned_cols=37 Identities=22% Similarity=0.163 Sum_probs=34.8
Q ss_pred cCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEE
Q 003176 33 GGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKY 69 (842)
Q Consensus 33 gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y 69 (842)
+|++.-+.|+.+.|..+|+++|++..+++++..+|=|
T Consensus 8 ~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~ 44 (74)
T cd01813 8 GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLG 44 (74)
T ss_pred CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEe
Confidence 6788889999999999999999999999999899998
No 73
>cd01802 AN1_N ubiquitin-like domain of AN1. AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.
Probab=60.83 E-value=17 Score=32.97 Aligned_cols=42 Identities=12% Similarity=0.129 Sum_probs=38.2
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
++-.+|++..+.|+.+.|=.+|+++|++..|++.+...|-|.
T Consensus 32 Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~ 73 (103)
T cd01802 32 IETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWN 73 (103)
T ss_pred EEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEEC
Confidence 356689999999999999999999999999999988899885
No 74
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=57.74 E-value=6.2 Score=45.79 Aligned_cols=23 Identities=35% Similarity=0.745 Sum_probs=18.1
Q ss_pred ccceEeCCCCCcCCcCc--CCCCCC
Q 003176 819 EHRTVTCTKCKGIGHNK--LSCKET 841 (842)
Q Consensus 819 ~kr~~~Cs~C~~~GHN~--~tC~~~ 841 (842)
...+++|++|||.||=+ +.||.-
T Consensus 934 K~Ttr~C~nCGQvGHmkTNK~CP~f 958 (968)
T COG5179 934 KNTTRTCGNCGQVGHMKTNKACPKF 958 (968)
T ss_pred CCcceecccccccccccccccCccc
Confidence 34689999999999976 468753
No 75
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=55.77 E-value=5.1 Score=22.26 Aligned_cols=9 Identities=22% Similarity=0.243 Sum_probs=3.4
Q ss_pred CCCCCCccc
Q 003176 803 RTPTTHQKR 811 (842)
Q Consensus 803 r~~GRPKkk 811 (842)
|++|||++.
T Consensus 2 r~RGRP~k~ 10 (13)
T PF02178_consen 2 RKRGRPRKN 10 (13)
T ss_dssp --SS--TT-
T ss_pred CcCCCCccc
Confidence 678999875
No 76
>cd01804 midnolin_N Ubiquitin-like domain of midnolin. midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.
Probab=53.92 E-value=29 Score=29.62 Aligned_cols=41 Identities=15% Similarity=0.240 Sum_probs=34.8
Q ss_pred EeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 30 SYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 30 ~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
+-..|++..+.|+.+.|-.||+.+|++..++......|-|.
T Consensus 7 k~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~ 47 (78)
T cd01804 7 HSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHR 47 (78)
T ss_pred EECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEEC
Confidence 34568889999999999999999999999988877777654
No 77
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=52.12 E-value=34 Score=27.98 Aligned_cols=39 Identities=23% Similarity=0.359 Sum_probs=36.0
Q ss_pred ecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 32 DGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 32 ~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
..|.+.-+.|+.+.+-.+|+.+|++..+++.+.+.|-|.
T Consensus 3 ~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~ 41 (69)
T PF00240_consen 3 LSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYN 41 (69)
T ss_dssp TTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEET
T ss_pred CCCcEEEEEECCCCCHHHhhhhcccccccccccceeeee
Confidence 468899999999999999999999999999999998883
No 78
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=50.40 E-value=50 Score=30.15 Aligned_cols=80 Identities=11% Similarity=0.165 Sum_probs=50.5
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcce-EEEEecCC--CCCceEeecChHHHHHHHhccCCceeEEEEE-
Q 003176 29 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSL-SVKYFLPG--NKQTLITICNDKDLKRMFDFHEGSVTADVFV- 104 (842)
Q Consensus 29 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~-~~~y~l~~--~~~~l~~~~~d~dl~~m~~~~~~~~~~~v~~- 104 (842)
.-+.+|.||.|-|..=-+-.|.+.|+.++||+....- =--|.|-+ .++.-+-.=+|.+|..+....+...+-|+.+
T Consensus 5 ~I~~dG~tk~VNV~~c~~a~eI~~rvLKKfg~~~~~~~~~~~v~d~~~~~~~~~~~LsD~EL~~IC~s~~r~er~Rlilr 84 (105)
T PF14847_consen 5 FILEDGSTKTVNVSGCFNAQEIKRRVLKKFGLPEHPRNYCFYVLDGESPDPSNCRPLSDVELVTICHSPDRPERNRLILR 84 (105)
T ss_dssp EEETTTEEEEEE--S--HHHHHHHHHHHHHTSS--CCCEEEEEE-S-----SSEEEE-SSHHHHHHHTT--SSS--EEE-
T ss_pred EECCCCcEEEEEECCCCCHHHHHHHHHHHcCCccccccceEEEecccccccccceECcHHHHHHHHcCCCCccccceEEE
Confidence 4578999999999999999999999999999876211 12244444 2244444556788999999999999999999
Q ss_pred -eccC
Q 003176 105 -IGTS 108 (842)
Q Consensus 105 -~~~~ 108 (842)
++..
T Consensus 85 k~~~~ 89 (105)
T PF14847_consen 85 KVHKG 89 (105)
T ss_dssp -EESS
T ss_pred ecCCC
Confidence 6655
No 79
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=43.52 E-value=13 Score=24.65 Aligned_cols=12 Identities=17% Similarity=0.210 Sum_probs=9.3
Q ss_pred CCCCCCCccccc
Q 003176 802 TRTPTTHQKRRR 813 (842)
Q Consensus 802 ~r~~GRPKkkR~ 813 (842)
.|++|||+|...
T Consensus 1 kRkRGRPrK~~~ 12 (26)
T smart00384 1 KRKRGRPRKAPK 12 (26)
T ss_pred CCCCCCCCCCCC
Confidence 368999998754
No 80
>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF. NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.
Probab=42.67 E-value=45 Score=28.52 Aligned_cols=41 Identities=24% Similarity=0.337 Sum_probs=34.3
Q ss_pred EeecCce-EEE-EeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 30 SYDGGEA-NAV-AINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 30 ~y~gg~~-~~~-~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
+-..|++ ..+ .|+.+.|-++|+++|++..|++.+...|-|.
T Consensus 6 k~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~ 48 (78)
T cd01797 6 RTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYR 48 (78)
T ss_pred EcCCCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeC
Confidence 4456776 457 4899999999999999999999998899885
No 81
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=39.94 E-value=14 Score=38.60 Aligned_cols=23 Identities=39% Similarity=0.810 Sum_probs=19.2
Q ss_pred ccccccchhccCCchhhHHHHHHhcC
Q 003176 724 RDCSCLVWKATGLPCHHAIAVFNSTG 749 (842)
Q Consensus 724 ~~CsC~~~~~~GiPC~Halav~~~~~ 749 (842)
..|||..|. .||.|+-||.-..+
T Consensus 125 ~dCSCPD~a---nPCKHi~AvyY~la 147 (266)
T COG4279 125 TDCSCPDYA---NPCKHIAAVYYLLA 147 (266)
T ss_pred cccCCCCcc---cchHHHHHHHHHHH
Confidence 479999887 69999999977654
No 82
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=39.29 E-value=23 Score=31.37 Aligned_cols=27 Identities=15% Similarity=0.363 Sum_probs=18.2
Q ss_pred CCCCCCCCCCcccccccCCCccceEeCCCCCc
Q 003176 799 PSSTRTPTTHQKRRRKILGIEHRTVTCTKCKG 830 (842)
Q Consensus 799 P~~~r~~GRPKkkR~~~~~~~kr~~~Cs~C~~ 830 (842)
|.++|..||-|+.|- .-+.++|++|+.
T Consensus 2 ~kKRrn~GR~K~~rG-----hv~~V~C~nCgr 28 (95)
T PRK09335 2 PKKRENRGRRKGDKG-----HVGYVQCDNCGR 28 (95)
T ss_pred CcccccCCCCCCCCC-----CCccEEeCCCCC
Confidence 456677787776542 224689999986
No 83
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=38.73 E-value=62 Score=27.34 Aligned_cols=38 Identities=26% Similarity=0.348 Sum_probs=34.6
Q ss_pred cCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003176 33 GGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 70 (842)
Q Consensus 33 gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 70 (842)
.|.+..+.|+.+.|-.||+.+|++..+++.+...|-|.
T Consensus 10 ~Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~ 47 (73)
T cd01791 10 LGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKW 47 (73)
T ss_pred CCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeC
Confidence 47888889999999999999999999999998888885
No 84
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=37.93 E-value=17 Score=27.37 Aligned_cols=19 Identities=37% Similarity=0.809 Sum_probs=16.8
Q ss_pred eEeCCCCCcCCcCcCCCCC
Q 003176 822 TVTCTKCKGIGHNKLSCKE 840 (842)
Q Consensus 822 ~~~Cs~C~~~GHN~~tC~~ 840 (842)
...|.+|++.||-..-||+
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 3589999999999999993
No 85
>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2. hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.
Probab=37.28 E-value=67 Score=26.65 Aligned_cols=36 Identities=11% Similarity=0.254 Sum_probs=31.2
Q ss_pred cCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEE
Q 003176 33 GGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKY 69 (842)
Q Consensus 33 gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y 69 (842)
.|.+ .+.|+.+.|=.+|+.++++..+++.+...+-|
T Consensus 9 ~g~~-~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li~ 44 (71)
T cd01808 9 KDKE-EIEIAEDASVKDFKEAVSKKFKANQEQLVLIF 44 (71)
T ss_pred CCCE-EEEECCCChHHHHHHHHHHHhCCCHHHEEEEE
Confidence 4554 78999999999999999999998888788776
No 86
>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=37.15 E-value=59 Score=27.80 Aligned_cols=38 Identities=16% Similarity=0.232 Sum_probs=33.2
Q ss_pred EeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEE
Q 003176 30 SYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSV 67 (842)
Q Consensus 30 ~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~ 67 (842)
+-.+|++-.+.|+.+.|=.||+.++++..+++.+...|
T Consensus 8 k~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL 45 (80)
T cd01792 8 KMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRL 45 (80)
T ss_pred EeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEE
Confidence 44568898899999999999999999999988887766
No 87
>PLN00186 ribosomal protein S26; Provisional
Probab=33.69 E-value=31 Score=31.28 Aligned_cols=27 Identities=15% Similarity=0.437 Sum_probs=18.0
Q ss_pred CCCCCCCCCCcccccccCCCccceEeCCCCCc
Q 003176 799 PSSTRTPTTHQKRRRKILGIEHRTVTCTKCKG 830 (842)
Q Consensus 799 P~~~r~~GRPKkkR~~~~~~~kr~~~Cs~C~~ 830 (842)
|.++|..||-|+.|- .-+.++|++|+.
T Consensus 2 ~kKRrN~GR~K~~rG-----hv~~V~C~nCgr 28 (109)
T PLN00186 2 TKKRRNGGRNKHGRG-----HVKRIRCSNCGK 28 (109)
T ss_pred CcccccCCCCCCCCC-----CCcceeeCCCcc
Confidence 456667777775542 224679999986
No 88
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=33.33 E-value=32 Score=31.21 Aligned_cols=27 Identities=22% Similarity=0.463 Sum_probs=18.2
Q ss_pred CCCCCCCCCCcccccccCCCccceEeCCCCCc
Q 003176 799 PSSTRTPTTHQKRRRKILGIEHRTVTCTKCKG 830 (842)
Q Consensus 799 P~~~r~~GRPKkkR~~~~~~~kr~~~Cs~C~~ 830 (842)
|.++|..||-|+.|- .-+.++|.+|+.
T Consensus 2 ~kKRrN~GR~K~~rG-----hv~~V~C~nCgr 28 (108)
T PTZ00172 2 TSKRRNNGRSKHGRG-----HVKPVRCSNCGR 28 (108)
T ss_pred CcccccCCCCCCCCC-----CCccEEeCCccc
Confidence 456677787775542 224689999986
No 89
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=31.79 E-value=18 Score=28.90 Aligned_cols=20 Identities=30% Similarity=0.710 Sum_probs=8.8
Q ss_pred ceEeCCCCCcCC---cCcCCCCC
Q 003176 821 RTVTCTKCKGIG---HNKLSCKE 840 (842)
Q Consensus 821 r~~~Cs~C~~~G---HN~~tC~~ 840 (842)
|.+.|..|+..| |..+-||.
T Consensus 32 r~y~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 32 RKYVCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp GG---TTT---GGG---GGG-TT
T ss_pred hcCcCCCCcCcCccccccccCcC
Confidence 568999999866 88888985
No 90
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=31.56 E-value=68 Score=27.35 Aligned_cols=29 Identities=17% Similarity=0.372 Sum_probs=25.7
Q ss_pred eeCCHHHHHHHHHHHHHhcceeEEEEeeC
Q 003176 280 EFKSVIEFRDALQRFSIAHRFRYKFKKNE 308 (842)
Q Consensus 280 ~F~s~ee~k~ai~~yAi~~gf~~r~~ks~ 308 (842)
.|+|.+++..+|..|+.+++-.+.+.+.+
T Consensus 13 ~yPs~e~i~~aIE~YC~~~~~~l~Fisr~ 41 (74)
T PF14201_consen 13 KYPSKEEICEAIEKYCIKNGESLEFISRD 41 (74)
T ss_pred CCCCHHHHHHHHHHHHHHcCCceEEEecC
Confidence 48999999999999999999999986543
No 91
>KOG3206 consensus Alpha-tubulin folding cofactor B [Posttranslational modification, protein turnover, chaperones]
Probab=30.31 E-value=61 Score=33.00 Aligned_cols=62 Identities=18% Similarity=0.202 Sum_probs=45.3
Q ss_pred eCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCCceeEEEEEec
Q 003176 41 INPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEGSVTADVFVIG 106 (842)
Q Consensus 41 v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~~~~~~v~~~~ 106 (842)
.+++||..+|+.||.-.+|...++ ++-||-..+|.+++.-+++|-. +-|...+.-+||-|+-
T Consensus 19 ~~~~ltl~q~K~KLe~~~G~~~~~--M~l~l~~~~d~~~~~lsn~d~~--lg~~~~~Dg~rihviD 80 (234)
T KOG3206|consen 19 LSNSLTLAQFKDKLELLTGTEAES--MELELYDGDDKKVSALSNEDAD--LGFYKVEDGLRIHVID 80 (234)
T ss_pred cCCcCcHHHHHhhhhhhhCCCccc--eEEEEEcCCCceeeeccCCccc--ccccCCCCceEEEEEe
Confidence 478999999999999999988875 5557878888888877776632 3344333346766655
No 92
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=29.85 E-value=27 Score=35.18 Aligned_cols=16 Identities=31% Similarity=0.777 Sum_probs=13.6
Q ss_pred EeCCCCCcCCcCcCCC
Q 003176 823 VTCTKCKGIGHNKLSC 838 (842)
Q Consensus 823 ~~Cs~C~~~GHN~~tC 838 (842)
..|.+||+.||-++-|
T Consensus 98 ~~C~~Cg~~GH~~~dC 113 (190)
T COG5082 98 KKCYNCGETGHLSRDC 113 (190)
T ss_pred cccccccccCcccccc
Confidence 5788888888888888
No 93
>PF13592 HTH_33: Winged helix-turn helix
Probab=29.84 E-value=58 Score=26.27 Aligned_cols=28 Identities=39% Similarity=0.447 Sum_probs=24.0
Q ss_pred CCCChhHHHHHHHHhcCcccchhhhHHH
Q 003176 373 PHHKPKEISKSILRDFGVTLNYSQVYRG 400 (842)
Q Consensus 373 ~~~~~~~I~~~l~~~~g~~~sy~~~~ra 400 (842)
.-++.++|...|.++||+.++.+.+|+.
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~~~v~~l 30 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSPSGVYRL 30 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcHHHHHHH
Confidence 3467889999999999999999888865
No 94
>PHA00689 hypothetical protein
Probab=29.63 E-value=29 Score=26.61 Aligned_cols=14 Identities=50% Similarity=1.030 Sum_probs=11.2
Q ss_pred ccceEeCCCCCcCC
Q 003176 819 EHRTVTCTKCKGIG 832 (842)
Q Consensus 819 ~kr~~~Cs~C~~~G 832 (842)
..|..+|.+|++.|
T Consensus 14 epravtckrcgktg 27 (62)
T PHA00689 14 EPRAVTCKRCGKTG 27 (62)
T ss_pred CcceeehhhccccC
Confidence 34678999999876
No 95
>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.
Probab=29.35 E-value=55 Score=28.24 Aligned_cols=29 Identities=31% Similarity=0.527 Sum_probs=19.8
Q ss_pred EEeCCCCChHHHHHHHHHHhCCCCcceEE
Q 003176 39 VAINPETHFGDLKLKLAELLNLEYKSLSV 67 (842)
Q Consensus 39 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~ 67 (842)
|.|+.+-++++|..||.+.++++..++++
T Consensus 18 ie~~~~~t~~~L~~kI~~~l~~~~~~~~L 46 (80)
T PF11543_consen 18 IEVSPSSTLSDLKEKISEQLSIPDSSQSL 46 (80)
T ss_dssp EEE-TTSBHHHHHHHHHHHS---TTT---
T ss_pred EEcCCcccHHHHHHHHHHHcCCCCcceEE
Confidence 46899999999999999999988765555
No 96
>PF12762 DDE_Tnp_IS1595: ISXO2-like transposase domain; InterPro: IPR024445 This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2.
Probab=28.73 E-value=1.2e+02 Score=29.00 Aligned_cols=69 Identities=12% Similarity=0.116 Sum_probs=40.2
Q ss_pred CeEEeccccccccc--------------cceEEEEEEecCC-CCeEEEEEEEecCCChhhHHHHHHHHHHhhcCCCcEEE
Q 003176 465 PLLFLDSTSLRSKY--------------HEILLTATALDGD-DCIFPVAFAIVDTENDDSWNWFLEELRSAVSSSRSITF 529 (842)
Q Consensus 465 ~vl~iD~T~~~~~y--------------~~~Ll~a~g~D~~-~~~~plafalv~~Et~es~~WfL~~lk~~~~~~~p~~i 529 (842)
.+|-+|-||..++- .....++++++-+ +..--+-..++.+.+.++..-+++.... +..+|
T Consensus 4 G~VEiDEty~~~~~~~~~~~~~~~gr~~~~k~~V~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i~~~i~-----~gs~i 78 (151)
T PF12762_consen 4 GIVEIDETYFGGRKNKKPRRKGKRGRGSKNKVPVFGAVERNDGGTGRVFMFVVPDRSAETLKPIIQEHIE-----PGSTI 78 (151)
T ss_pred CEEEeCcCEECCcccccccCCCCCCCcCCCCcEEEEEEeecccCCceEEEEeecccccchhHHHHHHhhh-----cccee
Confidence 36667777765322 2233444444444 4344444556677888887666654322 34679
Q ss_pred EecCchhHH
Q 003176 530 VSDKQKGLM 538 (842)
Q Consensus 530 isD~~~~l~ 538 (842)
+||+..+-.
T Consensus 79 ~TD~~~aY~ 87 (151)
T PF12762_consen 79 ITDGWRAYN 87 (151)
T ss_pred eecchhhcC
Confidence 999998764
No 97
>PRK13907 rnhA ribonuclease H; Provisional
Probab=27.32 E-value=4.8e+02 Score=24.02 Aligned_cols=77 Identities=10% Similarity=0.100 Sum_probs=44.4
Q ss_pred eEEeccccccccccceEEEEEEecCCCCeEEEEE-EEecCCChhhHHHHHHHHHHhhcC-CCcEEEEecCchhHHHHHHh
Q 003176 466 LLFLDSTSLRSKYHEILLTATALDGDDCIFPVAF-AIVDTENDDSWNWFLEELRSAVSS-SRSITFVSDKQKGLMESVLK 543 (842)
Q Consensus 466 vl~iD~T~~~~~y~~~Ll~a~g~D~~~~~~plaf-alv~~Et~es~~WfL~~lk~~~~~-~~p~~iisD~~~~l~~AI~~ 543 (842)
.|.+||.+..+.-.+-.-.++ .|..+... +.+ .-..+.+..-|.-++..|+.+... ..++.|-||- +.+.+++..
T Consensus 3 ~iy~DGa~~~~~g~~G~G~vi-~~~~~~~~-~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS-~~vi~~~~~ 79 (128)
T PRK13907 3 EVYIDGASKGNPGPSGAGVFI-KGVQPAVQ-LSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDS-QLVERAVEK 79 (128)
T ss_pred EEEEeeCCCCCCCccEEEEEE-EECCeeEE-EEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEech-HHHHHHHhH
Confidence 378899988764333222222 45555432 332 222345566677777777777543 3567788886 556666666
Q ss_pred hc
Q 003176 544 IF 545 (842)
Q Consensus 544 vf 545 (842)
.+
T Consensus 80 ~~ 81 (128)
T PRK13907 80 EY 81 (128)
T ss_pred HH
Confidence 54
No 98
>cd01760 RBD Ubiquitin-like domain of RBD-like S/T kinases. The ras-binding domain (RBD) of the serine/threonine kinase raf is structurally quite similar to the beta-grasp fold of ubiquitin. A raf-like RBD is also present in RGS12 and other members of a family of GTPase activating proteins and TIAM1, a guanine nucleotide exchange protein.
Probab=25.85 E-value=1.2e+02 Score=25.63 Aligned_cols=37 Identities=19% Similarity=0.237 Sum_probs=31.6
Q ss_pred cCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEE
Q 003176 33 GGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKY 69 (842)
Q Consensus 33 gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y 69 (842)
-|.+-.+.|..++|-.|..+++|++-|++...+.+.-
T Consensus 8 ng~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~ 44 (72)
T cd01760 8 NGQRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFL 44 (72)
T ss_pred CCCeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEE
Confidence 3677889999999999999999999999987665544
No 99
>KOG1769 consensus Ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones]
Probab=24.92 E-value=1.5e+02 Score=26.71 Aligned_cols=38 Identities=21% Similarity=0.241 Sum_probs=34.5
Q ss_pred ecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEE
Q 003176 32 DGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKY 69 (842)
Q Consensus 32 ~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y 69 (842)
.+|.+...-|.|+..++-|++--|+.-|++.+++.|-|
T Consensus 28 qd~~~~~Fkikr~t~LkKLM~aYc~r~Gl~~~s~RFlF 65 (99)
T KOG1769|consen 28 QDGSVVVFKIKRHTPLKKLMKAYCERQGLSMNSLRFLF 65 (99)
T ss_pred CCCCEEEEEeecCChHHHHHHHHHHHcCCccceEEEEE
Confidence 46788899999999999999999999999999888776
No 100
>KOG3606 consensus Cell polarity protein PAR6 [Signal transduction mechanisms]
Probab=24.65 E-value=90 Score=33.06 Aligned_cols=85 Identities=14% Similarity=0.216 Sum_probs=63.6
Q ss_pred cCceEEEEeCCC--CChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCCceeEEEEEeccCCC
Q 003176 33 GGEANAVAINPE--THFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEGSVTADVFVIGTSGF 110 (842)
Q Consensus 33 gg~~~~~~v~~~--~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~~~~~~v~~~~~~~~ 110 (842)
|-|-|=.+++|+ -+|.+|-+-+...-.|..-.+++-|.=+. --|.+|.||+-|.+-++.-. .-+||||=.+.+.
T Consensus 26 daEfRRfsl~r~~~~~f~~F~~Lv~~~H~i~nvdvllgY~d~h--gDLLPinNDDn~~ka~~sa~--PlLR~~iQkr~ea 101 (358)
T KOG3606|consen 26 DAEFRRFSLPRHSASSFDEFYSLVEHLHHIPNVDVLLGYADTH--GDLLPINNDDNLHKALSSAR--PLLRLLIQKREEA 101 (358)
T ss_pred cchhheecccccCcccHHHHHHHHHHHhcCCCceEEEEEecCC--CceecccCchhHHHHhhccC--chhhhhhhhhhhh
Confidence 445566677776 48999998888877888778999997666 45999999999999988653 3599999988766
Q ss_pred ccchhhhhccc
Q 003176 111 DREAFAIETGR 121 (842)
Q Consensus 111 ~~~~~~~~~~~ 121 (842)
|.+-++...+.
T Consensus 102 ~~~~~~fgt~s 112 (358)
T KOG3606|consen 102 DEEKYGFGTDS 112 (358)
T ss_pred hhhccCccccc
Confidence 65543444443
No 101
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=24.19 E-value=1.7e+02 Score=34.44 Aligned_cols=44 Identities=23% Similarity=0.362 Sum_probs=30.2
Q ss_pred ceEEEEcCcee--Eeec----CCccccccchhccCCchhhHHHHHHhcCCCc
Q 003176 707 TLFEVQGDSTH--VVDM----NKRDCSCLVWKATGLPCHHAIAVFNSTGRNV 752 (842)
Q Consensus 707 ~~feV~~~~~~--~V~l----~~~~CsC~~~~~~GiPC~Halav~~~~~~~~ 752 (842)
-..+|.+.+.| .|.+ -+..|||.. ...| =|.|++||+...-..|
T Consensus 50 v~A~V~Gs~~y~v~vtL~~~~~ss~CTCP~-~~~g-aCKH~VAvvl~~~~~p 99 (587)
T COG4715 50 VRAVVEGSRRYRVRVTLEGGALSSICTCPY-GGSG-ACKHVVAVVLEYLDDP 99 (587)
T ss_pred EEEEEeccceeeEEEEeecCCcCceeeCCC-CCCc-chHHHHHHHHHHhhcc
Confidence 35667776554 4555 357899997 5554 4999999988765443
No 102
>smart00455 RBD Raf-like Ras-binding domain.
Probab=23.53 E-value=1.4e+02 Score=24.94 Aligned_cols=36 Identities=17% Similarity=0.180 Sum_probs=30.5
Q ss_pred CceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEE
Q 003176 34 GEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKY 69 (842)
Q Consensus 34 g~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y 69 (842)
|.+-.+.|..+++-.|...+++++.|++...+.+.-
T Consensus 9 ~~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~ 44 (70)
T smart00455 9 NQRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRL 44 (70)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEE
Confidence 566788899999999999999999999887665543
No 103
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=23.23 E-value=1.2e+02 Score=25.37 Aligned_cols=34 Identities=21% Similarity=0.251 Sum_probs=26.2
Q ss_pred CceEEEEeCCCCChHHHHHHHHHHhCCCCcceEE
Q 003176 34 GEANAVAINPETHFGDLKLKLAELLNLEYKSLSV 67 (842)
Q Consensus 34 g~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~ 67 (842)
|.+-.+.|..++|-.|+.++++++.|++...+.+
T Consensus 10 ~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V 43 (71)
T PF02196_consen 10 GQRTVVQVRPGMTIRDALSKACKKRGLNPECCDV 43 (71)
T ss_dssp TEEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEE
T ss_pred CCEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEE
Confidence 5667889999999999999999999998875443
No 104
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=22.79 E-value=77 Score=25.52 Aligned_cols=34 Identities=21% Similarity=0.344 Sum_probs=20.2
Q ss_pred CCCCCCCCCCcccccccCCCccceEeCCCCCcCC
Q 003176 799 PSSTRTPTTHQKRRRKILGIEHRTVTCTKCKGIG 832 (842)
Q Consensus 799 P~~~r~~GRPKkkR~~~~~~~kr~~~Cs~C~~~G 832 (842)
|..+.++.|..++|............|+.||..-
T Consensus 4 PKrk~S~srr~~RRsh~~l~~~~l~~C~~CG~~~ 37 (57)
T PRK12286 4 PKRKTSKSRKRKRRAHFKLKAPGLVECPNCGEPK 37 (57)
T ss_pred CcCcCChhhcchhcccccccCCcceECCCCCCcc
Confidence 4444555666565554333344566899998753
No 105
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=22.43 E-value=1.1e+02 Score=27.70 Aligned_cols=29 Identities=14% Similarity=0.266 Sum_probs=22.2
Q ss_pred CCceeCCHHHHHHHHHHHHHhcceeEEEEeeCc
Q 003176 277 VGQEFKSVIEFRDALQRFSIAHRFRYKFKKNET 309 (842)
Q Consensus 277 vG~~F~s~ee~k~ai~~yAi~~gf~~r~~ks~~ 309 (842)
+.+.|+|+|++. .||.++|..|.+.....
T Consensus 51 v~l~F~skE~Ai----~yaer~G~~Y~V~~p~~ 79 (101)
T PF04800_consen 51 VRLKFDSKEDAI----AYAERNGWDYEVEEPKK 79 (101)
T ss_dssp CEEEESSHHHHH----HHHHHCT-EEEEE-STT
T ss_pred eEeeeCCHHHHH----HHHHHcCCeEEEeCCCC
Confidence 889999998765 68999999998865443
No 106
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=22.27 E-value=56 Score=27.16 Aligned_cols=36 Identities=22% Similarity=0.473 Sum_probs=15.8
Q ss_pred HHhHhhcCCCCChhHHHHHHHHhcCcccchhhhHHHH
Q 003176 365 IKDKLRESPHHKPKEISKSILRDFGVTLNYSQVYRGI 401 (842)
Q Consensus 365 ~~~~l~~~~~~~~~~I~~~l~~~~g~~~sy~~~~rak 401 (842)
+...++.+|..+..+|...+.+. |..+|...++|.-
T Consensus 4 I~~~v~~~p~~s~~~i~~~l~~~-~~~vS~~TI~r~L 39 (72)
T PF01498_consen 4 IVRMVRRNPRISAREIAQELQEA-GISVSKSTIRRRL 39 (72)
T ss_dssp ------------HHHHHHHT----T--S-HHHHHHHH
T ss_pred HHHHHHHCCCCCHHHHHHHHHHc-cCCcCHHHHHHHH
Confidence 44567788999999999999888 9999999998763
No 107
>PF08459 UvrC_HhH_N: UvrC Helix-hairpin-helix N-terminal; InterPro: IPR001162 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases. Proteins that contain the UvrC homology region 1, IPR000305 from INTERPRO, are listed below: Prokaryotic UvrC proteins. Bacteriophage T4 END2 protein. Small subunit of ribonucleotide reductase enzyme. T4 TEV1 protein. Endonuclease specific to the thymidylate synthase (td) gene splice junction. Found in putative intron-homing endonucleases encoded by group I introns of fungi and phage. Mycobacterium hypothetical protein Y002. Exonuclease by similarity. Bacillus subtilis hypothetical protein YURQ. ; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3C65_A 2NRZ_A 2NRR_A 2NRX_A 2NRV_A 2NRT_A 2NRW_A.
Probab=20.64 E-value=3.1e+02 Score=26.95 Aligned_cols=64 Identities=17% Similarity=0.314 Sum_probs=42.3
Q ss_pred eEEeccccccccccceEEEEEEecCCCCeEEEEEEEecCCChhhHHHHHHHHHHhhcC------CCcEEEEecCchhHHH
Q 003176 466 LLFLDSTSLRSKYHEILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSS------SRSITFVSDKQKGLME 539 (842)
Q Consensus 466 vl~iD~T~~~~~y~~~Ll~a~g~D~~~~~~plafalv~~Et~es~~WfL~~lk~~~~~------~~p~~iisD~~~~l~~ 539 (842)
|+|.||-+.++.|+- |-+-..+..+.|.-+-+.+.+.+.. .-|-.|+.|+.+|-.+
T Consensus 32 Vvf~~G~~~k~~YR~------------------f~i~~~~~~dDy~~M~Evl~RR~~~~~~~~~~lPDLilIDGG~gQl~ 93 (155)
T PF08459_consen 32 VVFENGKPDKSEYRR------------------FNIKTVDGGDDYAAMREVLTRRFKRLKEEKEPLPDLILIDGGKGQLN 93 (155)
T ss_dssp EEEETTEE-GGG-EE------------------EEEE--STT-HHHHHHHHHHHHHCCCHHHT----SEEEESSSHHHHH
T ss_pred EEEECCccChhhCce------------------EecCCCCCCcHHHHHHHHHHHHHhcccccCCCCCCEEEEcCCHHHHH
Confidence 567777777777764 2233334558888888888888753 2488999999999999
Q ss_pred HHHhhccc
Q 003176 540 SVLKIFEN 547 (842)
Q Consensus 540 AI~~vfP~ 547 (842)
|+.+++-.
T Consensus 94 aa~~~l~~ 101 (155)
T PF08459_consen 94 AAKEVLKE 101 (155)
T ss_dssp HHHHHHHC
T ss_pred HHHHHHHH
Confidence 99888653
No 108
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=20.63 E-value=45 Score=33.61 Aligned_cols=19 Identities=26% Similarity=0.655 Sum_probs=17.0
Q ss_pred ceEeCCCCCcCCcCcCCCC
Q 003176 821 RTVTCTKCKGIGHNKLSCK 839 (842)
Q Consensus 821 r~~~Cs~C~~~GHN~~tC~ 839 (842)
....|-+|++.||-++-||
T Consensus 59 ~~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 59 ENPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred cccccchhcccCcccccCC
Confidence 3568999999999999999
No 109
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=20.25 E-value=71 Score=28.19 Aligned_cols=34 Identities=15% Similarity=0.318 Sum_probs=27.9
Q ss_pred hhHHHHHHHHHHHHhhChhHHHHHHhhccccccc
Q 003176 588 ARLDSFRMSAEQVKKVSSNAFDWMMQIAPEYWTN 621 (842)
Q Consensus 588 ~t~~eFe~~~~~l~~~~~~~~~yL~~~~~~~Wa~ 621 (842)
.+..+|++.|..+.......++||..+.++.+..
T Consensus 5 ~~~~eF~~~w~~~~~~~~~~~~yL~~i~p~~l~~ 38 (94)
T PF13877_consen 5 KNSYEFERDWRRLKKDPEERYEYLKSIPPDSLPK 38 (94)
T ss_pred CCHHHHHHHHHHHcCCHHHHHHHHHhCChHHHHH
Confidence 3678999999999877778999999997766643
Done!